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Zhao X, Yu J, Chanda B, Zhao J, Wu S, Zheng Y, Sun H, Levi A, Ling KS, Fei Z. Genomic and pangenomic analyses provide insights into the population history and genomic diversification of bottle gourd. THE NEW PHYTOLOGIST 2024. [PMID: 38503725 DOI: 10.1111/nph.19673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Bottle gourd (Lagenaria siceraria (Mol.) Strandl.) is an economically important vegetable crop and one of the earliest domesticated crops. However, the population history and genomic diversification of bottle gourd have not been extensively studied. We generated a comprehensive bottle gourd genome variation map from genome sequences of 197 world-wide representative accessions, which enables a genome-wide association study for identifying genomic loci associated with resistance to zucchini yellow mosaic virus, and constructed a bottle gourd pangenome that harbors 1534 protein-coding genes absent in the reference genome. Demographic analyses uncover that domesticated bottle gourd originated in Southern Africa c. 12 000 yr ago, and subsequently radiated to the New World via the Atlantic drift and to Eurasia through the efforts of early farmers in the initial Holocene. The identified highly differentiated genomic regions among different bottle gourd populations harbor many genes contributing to their local adaptations such as those related to disease resistance and stress tolerance. Presence/absence variation analysis of genes in the pangenome reveals numerous genes including those involved in abiotic/biotic stress responses that have been under selection during the world-wide expansion of bottle gourds. The bottle gourd variation map and pangenome provide valuable resources for future functional studies and genomics-assisted breeding.
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Affiliation(s)
- Xuebo Zhao
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Jingyin Yu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Bidisha Chanda
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Jiantao Zhao
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Yi Zheng
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Levi
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Kai-Shu Ling
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
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Adam H, Gutiérrez A, Couderc M, Sabot F, Ntakirutimana F, Serret J, Orjuela J, Tregear J, Jouannic S, Lorieux M. Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture. BMC Genomics 2023; 24:587. [PMID: 37794325 PMCID: PMC10548634 DOI: 10.1186/s12864-023-09695-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud.). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The gene regulatory network that governs intra- and interspecific panicle diversity is still under-studied. RESULTS To identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapó. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12, QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits. CONCLUSION Our analysis led to the detection of genomic variations between O. sativa cv. Caiapó and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed.
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Affiliation(s)
- Hélène Adam
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
| | | | - Marie Couderc
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - François Sabot
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | | | - Julien Serret
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - Julie Orjuela
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - James Tregear
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - Stefan Jouannic
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
| | - Mathias Lorieux
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Cali, Colombia.
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Ntakirutimana F, Tranchant-Dubreuil C, Cubry P, Chougule K, Zhang J, Wing RA, Adam H, Lorieux M, Jouannic S. Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3 (BETHESDA, MD.) 2023; 13:jkad174. [PMID: 37535690 PMCID: PMC10542218 DOI: 10.1093/g3journal/jkad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023]
Abstract
African rice (Oryza glaberrima Steud), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3,000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses. While inflorescence architecture, a key trait for rice grain yield improvement, has been extensively studied in Asian rice, the morphological and genetic determinants of this complex trait are less understood in African rice. In this study, using a previously developed association panel of 162 O. glaberrima accessions and new SNP variants characterized through mapping to a new version of the O. glaberrima reference genome, we conducted a genome-wide association study of four major morphological panicle traits. We have found a total of 41 stable genomic regions that are significantly associated with these traits, of which 13 co-localized with previously identified QTLs in O. sativa populations and 28 were unique for this association panel. Additionally, we found a genomic region of interest on chromosome 3 that was associated with the number of spikelets and primary and secondary branches. Within this region was localized the O. sativa ortholog of the PHYTOCHROME B gene (Oglab_006903/OgPHYB). Haplotype analysis revealed the occurrence of natural sequence variants at the OgPHYB locus associated with panicle architecture variation through modulation of the flowering time phenotype, whereas no equivalent alleles were found in O. sativa. The identification in this study of genomic regions specific to O. glaberrima indicates panicle-related intra-specific genetic variation in this species, increasing our understanding of the underlying molecular processes governing panicle architecture. Identified candidate genes and major haplotypes may facilitate the breeding of new African rice cultivars with preferred panicle traits.
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Affiliation(s)
| | | | - Philippe Cubry
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Hélène Adam
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Mathias Lorieux
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Stefan Jouannic
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
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Robson JK, Ferguson JN, McAusland L, Atkinson JA, Tranchant-Dubreuil C, Cubry P, Sabot F, Wells DM, Price AH, Wilson ZA, Murchie EH. Chlorophyll fluorescence-based high-throughput phenotyping facilitates the genetic dissection of photosynthetic heat tolerance in African (Oryza glaberrima) and Asian (Oryza sativa) rice. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5181-5197. [PMID: 37347829 PMCID: PMC10498015 DOI: 10.1093/jxb/erad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/20/2023] [Indexed: 06/24/2023]
Abstract
Rising temperatures and extreme heat events threaten rice production. Half of the global population relies on rice for basic nutrition, and therefore developing heat-tolerant rice is essential. During vegetative development, reduced photosynthetic rates can limit growth and the capacity to store soluble carbohydrates. The photosystem II (PSII) complex is a particularly heat-labile component of photosynthesis. We have developed a high-throughput chlorophyll fluorescence-based screen for photosynthetic heat tolerance capable of screening hundreds of plants daily. Through measuring the response of maximum PSII efficiency to increasing temperature, this platform generates data for modelling the PSII-temperature relationship in large populations in a small amount of time. Coefficients from these models (photosynthetic heat tolerance traits) demonstrated high heritabilities across African (Oryza glaberrima) and Asian (Oryza sativa, Bengal Assam Aus Panel) rice diversity sets, highlighting valuable genetic variation accessible for breeding. Genome-wide association studies were performed across both species for these traits, representing the first documented attempt to characterize the genetic basis of photosynthetic heat tolerance in any species to date. A total of 133 candidate genes were highlighted. These were significantly enriched with genes whose predicted roles suggested influence on PSII activity and the response to stress. We discuss the most promising candidates for improving photosynthetic heat tolerance in rice.
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Affiliation(s)
- Jordan K Robson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - John N Ferguson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- School of Life Sciences, University of Essex, Colchester, UK
| | - Lorna McAusland
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Jonathan A Atkinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | | | - Phillipe Cubry
- Institut de Recherche pour le Developpement, 911 Av. Agropolis, 34394 Montpellier, France
| | - François Sabot
- Institut de Recherche pour le Developpement, 911 Av. Agropolis, 34394 Montpellier, France
| | - Darren M Wells
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Adam H Price
- Institut de Recherche pour le Developpement, 911 Av. Agropolis, 34394 Montpellier, France
| | - Zoe A Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Erik H Murchie
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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5
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Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, Edwards D, Odeny DA, Cheng S. Plant genome resequencing and population genomics: Current status and future prospects. MOLECULAR PLANT 2023; 16:1252-1268. [PMID: 37501370 DOI: 10.1016/j.molp.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
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Affiliation(s)
- Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weidong Ning
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 53007, China
| | - Mengyun Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Kun Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, Nairobi, Kenya
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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6
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Jing CY, Zhang FM, Wang XH, Wang MX, Zhou L, Cai Z, Han JD, Geng MF, Yu WH, Jiao ZH, Huang L, Liu R, Zheng XM, Meng QL, Ren NN, Zhang HX, Du YS, Wang X, Qiang CG, Zou XH, Gaut BS, Ge S. Multiple domestications of Asian rice. NATURE PLANTS 2023; 9:1221-1235. [PMID: 37550371 DOI: 10.1038/s41477-023-01476-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/04/2023] [Indexed: 08/09/2023]
Abstract
The origin of domesticated Asian rice (Oryza sativa L.) has been controversial for more than half a century. The debates have focused on two leading hypotheses: a single domestication event in China or multiple domestication events in geographically separate areas. These two hypotheses differ in their predicted history of genes/alleles selected during domestication. Here we amassed a dataset of 1,578 resequenced genomes, including an expanded sample of wild rice from throughout its geographic range. We identified 993 selected genes that generated phylogenetic trees on which japonica and indica formed a monophyletic group, suggesting that the domestication alleles of these genes originated only once in either japonica or indica. Importantly, the domestication alleles of most selected genes (~80%) stemmed from wild rice in China, but the domestication alleles of a substantial minority of selected genes (~20%) originated from wild rice in South and Southeast Asia, demonstrating separate domestication events of Asian rice.
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Affiliation(s)
- Chun-Yan Jing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Xia Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lian Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jing-Dan Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mu-Fan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Hao Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Hui Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao-Ming Zheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qing-Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ning-Ning Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Xiang Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Su Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Gen Qiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Hui Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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7
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Osnato M. Evolution of flowering time genes in rice: From the paleolithic to the anthropocene. PLANT, CELL & ENVIRONMENT 2023; 46:1046-1059. [PMID: 36411270 DOI: 10.1111/pce.14495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 06/16/2023]
Abstract
The evolutionary paths of humans and plants have crossed more than once throughout millennia. While agriculture contributed to the evolution of societies in prehistory, human selection of desirable traits contributed to the evolution of crops during centuries of cultivation. Among cereal crops, rice is currently grown around the globe and represents staple food for almost half of the world population. Over time, rice cultivation has expanded from subtropical to temperate regions thanks to artificial selection of mutants with impaired response to photoperiod. Additional regulatory mechanisms control flowering in response to diverse environmental cues, anticipating or delaying the floral transition to produce seeds in more favourable conditions. Nevertheless, the changing climate is threatening grain production because modern cultivars are sensitive to external fluctuations that go beyond their physiological range. One possibility to guarantee food production could be the exploitation of novel varieties obtained by crossing highly productive Asian rice with stress tolerant African rice. This review explores the genetic basis of the key traits that marked the long journey of rice cultivation from the end of the paleolithic to the anthropocene, with a focus on heading date. By 2050, will rice plants of the future flower in the outer space?
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Affiliation(s)
- Michela Osnato
- Institut de Ciència i Tecnologia Ambientals, Universitat Autónoma de Barcelona (ICTA-UAB), Bellaterra, Spain
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8
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Small ST, Costantini C, Sagnon N, Guelbeogo MW, Emrich SJ, Kern AD, Fontaine MC, Besansky NJ. Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito. Proc Natl Acad Sci U S A 2023; 120:e2219835120. [PMID: 36881629 PMCID: PMC10089221 DOI: 10.1073/pnas.2219835120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Species distributed across heterogeneous environments often evolve locally adapted ecotypes, but understanding of the genetic mechanisms involved in their formation and maintenance in the face of gene flow is incomplete. In Burkina Faso, the major African malaria mosquito Anopheles funestus comprises two strictly sympatric and morphologically indistinguishable yet karyotypically differentiated forms reported to differ in ecology and behavior. However, knowledge of the genetic basis and environmental determinants of An. funestus diversification was impeded by lack of modern genomic resources. Here, we applied deep whole-genome sequencing and analysis to test the hypothesis that these two forms are ecotypes differentially adapted to breeding in natural swamps versus irrigated rice fields. We demonstrate genome-wide differentiation despite extensive microsympatry, synchronicity, and ongoing hybridization. Demographic inference supports a split only ~1,300 y ago, closely following the massive expansion of domesticated African rice cultivation ~1,850 y ago. Regions of highest divergence, concentrated in chromosomal inversions, were under selection during lineage splitting, consistent with local adaptation. The origin of nearly all variations implicated in adaptation, including chromosomal inversions, substantially predates the ecotype split, suggesting that rapid adaptation was fueled mainly by standing genetic variation. Sharp inversion frequency differences likely facilitated adaptive divergence between ecotypes by suppressing recombination between opposing chromosomal orientations of the two ecotypes, while permitting free recombination within the structurally monomorphic rice ecotype. Our results align with growing evidence from diverse taxa that rapid ecological diversification can arise from evolutionarily old structural genetic variants that modify genetic recombination.
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Affiliation(s)
- Scott T. Small
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Carlo Costantini
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
- Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC), Université de Montpellier, CNRS 5290, Institute of Research for Development (IRD) 224, F-34394Montpellier, France
| | - N’Fale Sagnon
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
| | - Moussa W. Guelbeogo
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
| | - Scott J. Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN46556
| | - Andrew D. Kern
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Michael C. Fontaine
- Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC), Université de Montpellier, CNRS 5290, Institute of Research for Development (IRD) 224, F-34394Montpellier, France
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AGGroningen, The Netherlands
| | - Nora J. Besansky
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
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Zhao X, Guo Y, Kang L, Yin C, Bi A, Xu D, Zhang Z, Zhang J, Yang X, Xu J, Xu S, Song X, Zhang M, Li Y, Kear P, Wang J, Liu Z, Fu X, Lu F. Population genomics unravels the Holocene history of bread wheat and its relatives. NATURE PLANTS 2023; 9:403-419. [PMID: 36928772 DOI: 10.1038/s41477-023-01367-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 02/08/2023] [Indexed: 05/06/2023]
Abstract
Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accessions, we found that bread wheat originated from the southwest coast of the Caspian Sea and underwent a slow speciation process, lasting ~3,300 yr owing to persistent gene flow from its relatives. Soon after, bread wheat spread across Eurasia and reached Europe, South Asia and East Asia ~7,000 to ~5,000 yr ago, shaping a diversified but occasionally convergent adaptive landscape in novel environments. By contrast, the cultivated relatives of bread wheat experienced a population decline by ~82% over the past ~2,000 yr due to the food choice shift of humans. Further biogeographical modelling predicted a continued population shrinking of many bread wheat relatives in the coming decades because of their vulnerability to the changing climate. These findings will guide future efforts in protecting and utilizing wheat biodiversity to enhance global wheat production.
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Affiliation(s)
- Xuebo Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yafei Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lipeng Kang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Aoyue Bi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Daxing Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiliang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jijin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohan Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Song Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyue Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Ming Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Philip Kear
- International Potato Center-China Center for Asia and the Pacific, Beijing, China
| | - Jing Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
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10
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Applications and Prospects of CRISPR/Cas9-Mediated Base Editing in Plant Breeding. Curr Issues Mol Biol 2023; 45:918-935. [PMID: 36826004 PMCID: PMC9955079 DOI: 10.3390/cimb45020059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 system (Cas9) has been used at length to optimize multiple aspects of germplasm resources. However, large-scale genomic research has indicated that novel variations in crop plants are attributed to single-nucleotide polymorphisms (SNPs). Therefore, substituting single bases into a plant genome may produce desirable traits. Gene editing by CRISPR/Cas9 techniques frequently results in insertions-deletions (indels). Base editing allows precise single-nucleotide changes in the genome in the absence of double-strand breaks (DSBs) and donor repair templates (DRTs). Therefore, BEs have provided a new way of thinking about genome editing, and base editing techniques are currently being utilized to edit the genomes of many different organisms. As traditional breeding techniques and modern molecular breeding technologies complement each other, various genome editing technologies have emerged. How to realize the greater potential of BE applications is the question we need to consider. Here, we explain various base editings such as CBEs, ABEs, and CGBEs. In addition, the latest applications of base editing technologies in agriculture are summarized, including crop yield, quality, disease, and herbicide resistance. Finally, the challenges and future prospects of base editing technologies are presented. The aim is to provide a comprehensive overview of the application of BE in crop breeding to further improve BE and make the most of its value.
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11
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Su C, Xu Z, Shan X, Cai B, Zhao H, Zhang J. Cell-type-specific co-expression inference from single cell RNA-sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.13.520181. [PMID: 36561173 DOI: 10.1101/2022.04.07.487499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The inference of gene co-expressions from microarray and RNA-sequencing data has led to rich insights on biological processes and disease mechanisms. However, the bulk samples analyzed in most studies are a mixture of different cell types. As a result, the inferred co-expressions are confounded by varying cell type compositions across samples and only offer an aggregated view of gene regulations that may be distinct across different cell types. The advancement of single cell RNA-sequencing (scRNA-seq) technology has enabled the direct inference of co-expressions in specific cell types, facilitating our understanding of cell-type-specific biological functions. However, the high sequencing depth variations and measurement errors in scRNA-seq data present significant challenges in inferring cell-type-specific gene co-expressions, and these issues have not been adequately addressed in the existing methods. We propose a statistical approach, CS-CORE, for estimating and testing cell-type-specific co-expressions, built on a general expression-measurement model that explicitly accounts for sequencing depth variations and measurement errors in the observed single cell data. Systematic evaluations show that most existing methods suffer from inflated false positives and biased co-expression estimates and clustering analysis, whereas CS-CORE has appropriate false positive control, unbiased co-expression estimates, good statistical power and satisfactory performance in downstream co-expression analysis. When applied to analyze scRNA-seq data from postmortem brain samples from Alzheimer’s disease patients and controls and blood samples from COVID-19 patients and controls, CS-CORE identified cell-type-specific co-expressions and differential co-expressions that were more reproducible and/or more enriched for relevant biological pathways than those inferred from other methods.
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12
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Jian L, Yan J, Liu J. De Novo Domestication in the Multi-Omics Era. PLANT & CELL PHYSIOLOGY 2022; 63:1592-1606. [PMID: 35762778 DOI: 10.1093/pcp/pcac077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Most cereal crops were domesticated within the last 12,000 years and subsequently spread around the world. These crops have been nourishing the world by supplying a primary energy and nutrient source, thereby playing a critical role in determining the status of human health and sustaining the global population. Here, we review the major challenges of future agriculture and emphasize the utilization of wild germplasm. De novo domestication is one of the most straightforward strategies to manipulate domestication-related and/or other genes with known function, and thereby introduce desired traits into wild plants. We also summarize known causal variations and their corresponding pathways in order to better understand the genetic basis of crop evolution, and how this knowledge could facilitate de novo domestication. Indeed knowledge-driven de novo domestication has great potential for the development of new sustainable crops that have climate-resilient high yield with low resource input and meet individual nutrient needs. Finally, we discuss current opportunities for and barriers to knowledge-driven de novo domestication.
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Affiliation(s)
- Liumei Jian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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13
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Affortit P, Effa-Effa B, Ndoye MS, Moukouanga D, Luchaire N, Cabrera-Bosquet L, Perálvarez M, Pilloni R, Welcker C, Champion A, Gantet P, Diedhiou AG, Manneh B, Aroca R, Vadez V, Laplaze L, Cubry P, Grondin A. Physiological and genetic control of transpiration efficiency in African rice, Oryza glaberrima Steud. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5279-5293. [PMID: 35429274 DOI: 10.1093/jxb/erac156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Improving crop water use efficiency, the amount of carbon assimilated as biomass per unit of water used by a plant, is of major importance as water for agriculture becomes scarcer. In rice, the genetic bases of transpiration efficiency, the derivation of water use efficiency at the whole-plant scale, and its putative component trait transpiration restriction under high evaporative demand remain unknown. These traits were measured in 2019 in a panel of 147 African rice (Oryza glaberrima) genotypes known to be potential sources of tolerance genes to biotic and abiotic stresses. Our results reveal that higher transpiration efficiency is associated with transpiration restriction in African rice. Detailed measurements in a subset of highly contrasted genotypes in terms of biomass accumulation and transpiration confirmed these associations and suggested that root to shoot ratio played an important role in transpiration restriction. Genome wide association studies identified marker-trait associations for transpiration response to evaporative demand, transpiration efficiency, and its residuals, with links to genes involved in water transport and cell wall patterning. Our data suggest that root-shoot partitioning is an important component of transpiration restriction that has a positive effect on transpiration efficiency in African rice. Both traits are heritable and define targets for breeding rice with improved water use strategies.
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Affiliation(s)
- Pablo Affortit
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Branly Effa-Effa
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CENAREST, Libreville, Gabon
| | - Mame Sokhatil Ndoye
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CERAAS, Thiès, Senegal
| | | | - Nathalie Luchaire
- LEPSE, Université de Montpellier, INRAE, Institut Agro, Montpellier, France
| | | | | | - Raphaël Pilloni
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Claude Welcker
- LEPSE, Université de Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Antony Champion
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Pascal Gantet
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | | | | | | | - Vincent Vadez
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CERAAS, Thiès, Senegal
- LMI LAPSE, Dakar, Senegal
- ICRISAT, Patancheru, India
| | - Laurent Laplaze
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LMI LAPSE, Dakar, Senegal
| | - Philippe Cubry
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Alexandre Grondin
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CERAAS, Thiès, Senegal
- LMI LAPSE, Dakar, Senegal
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14
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Pérez-Escobar OA, Tusso S, Przelomska NAS, Wu S, Ryan P, Nesbitt M, Silber MV, Preick M, Fei Z, Hofreiter M, Chomicki G, Renner SS. Genome sequencing of up to 6,000-yr-old Citrullus seeds reveals use of a bitter-fleshed species prior to watermelon domestication. Mol Biol Evol 2022; 39:6652436. [PMID: 35907246 PMCID: PMC9387916 DOI: 10.1093/molbev/msac168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Iconographic evidence from Egypt suggests that watermelon pulp was consumed there as a dessert by 4,360 BP. Earlier archaeobotanical evidence comes from seeds from Neolithic settlements in Libya, but whether these were watermelons with sweet pulp or other forms is unknown. We generated genome sequences from 6,000- and 3,300-year-old seeds from Libya and Sudan, and from worldwide herbarium collections made between 1824 and 2019, and analyzed these data together with resequenced genomes from important germplasm collections for a total of 131 accessions. Phylogenomic and population-genomic analyses reveal that (1) much of the nuclear genome of both ancient seeds is traceable to West African seed-use “egusi-type” watermelon (Citrullus mucosospermus) rather than domesticated pulp-use watermelon (Citrullus lanatus ssp. vulgaris); (2) the 6,000-year-old watermelon likely had bitter pulp and greenish-white flesh as today found in C. mucosospermus, given alleles in the bitterness regulators ClBT and in the red color marker LYCB; and (3) both ancient genomes showed admixture from C. mucosospermus, C. lanatus ssp. cordophanus, C. lanatus ssp. vulgaris, and even South African Citrullus amarus, and evident introgression between the Libyan seed (UMB-6) and populations of C. lanatus. An unexpected new insight is that Citrullus appears to have initially been collected or cultivated for its seeds, not its flesh, consistent with seed damage patterns induced by human teeth in the oldest Libyan material.
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Affiliation(s)
| | - Sergio Tusso
- Faculty of Biology, Division of Genetics, University of Munich (LMU), 82152 Planegg- Martinsried, Germany
| | | | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | | | - Mark Nesbitt
- Royal Botanic Gardens, Kew, TW9 3AE, United Kingdom
| | - Martina V Silber
- Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU), 80638 Munich, Germany
| | - Michaela Preick
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA.,USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Michael Hofreiter
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Guillaume Chomicki
- Ecology and Evolutionary Biology, School of Bioscience, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Susanne S Renner
- Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU), 80638 Munich, Germany.,Department of Biology, Washington University, Saint Louis, MO 63130, USA
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15
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Shang L, Li X, He H, Yuan Q, Song Y, Wei Z, Lin H, Hu M, Zhao F, Zhang C, Li Y, Gao H, Wang T, Liu X, Zhang H, Zhang Y, Cao S, Yu X, Zhang B, Zhang Y, Tan Y, Qin M, Ai C, Yang Y, Zhang B, Hu Z, Wang H, Lv Y, Wang Y, Ma J, Wang Q, Lu H, Wu Z, Liu S, Sun Z, Zhang H, Guo L, Li Z, Zhou Y, Li J, Zhu Z, Xiong G, Ruan J, Qian Q. A super pan-genomic landscape of rice. Cell Res 2022; 32:878-896. [PMID: 35821092 PMCID: PMC9525306 DOI: 10.1038/s41422-022-00685-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/10/2022] [Indexed: 01/09/2023] Open
Abstract
Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.
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Affiliation(s)
- Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
| | - Xiaoxia Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Huiying He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Qiaoling Yuan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yanni Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Zhaoran Wei
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Hai Lin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Min Hu
- State Key Laboratory for Agrobiotechnology, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Fengli Zhao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Chao Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yuhua Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Hongsheng Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Tianyi Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xiangpei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Hong Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Ya Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Shuaimin Cao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xiaoman Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Bintao Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yong Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yiqing Tan
- Academy for Advanced Interdisciplinary Studies, Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Mao Qin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Cheng Ai
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yingxue Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Bin Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Hongru Wang
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Yang Lv
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.,State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Yuexing Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Jie Ma
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Quan Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Hongwei Lu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | | | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yongfeng Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zuofeng Zhu
- State Key Laboratory for Agrobiotechnology, National Center for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China.
| | - Guosheng Xiong
- Academy for Advanced Interdisciplinary Studies, Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China. .,State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China.
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16
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de la Fuente Cantó C, Vigouroux Y. Evaluation of nine statistics to identify QTLs in bulk segregant analysis using next generation sequencing approaches. BMC Genomics 2022; 23:490. [PMID: 35794552 PMCID: PMC9258084 DOI: 10.1186/s12864-022-08718-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/20/2022] [Indexed: 11/22/2022] Open
Abstract
Background Bulk segregant analysis (BSA) combined with next generation sequencing is a powerful tool to identify quantitative trait loci (QTL). The impact of the size of the study population and the percentage of extreme genotypes analysed have already been assessed. But a good comparison of statistical approaches designed to identify QTL regions using next generation sequencing (NGS) technologies for BSA is still lacking. Results We developed an R code to simulate QTLs in bulks of F2 contrasted lines. We simulated a range of recombination rates based on estimations using different crop species. The simulations were used to benchmark the ability of statistical methods identify the exact location of true QTLs. A single QTL led to a shift in allele frequency across a large fraction of the chromosome for plant species with low recombination rate. The smoothed version of all statistics performed best notably the smoothed Euclidean distance-based statistics was always found to be more accurate in identifying the location of QTLs. We propose a simulation approach to build confidence interval statistics for the detection of QTLs. Conclusion We highlight the statistical methods best suited for BSA studies using NGS technologies in crops even when recombination rate is low. We also provide simulation codes to build confidence intervals and to assess the impact of recombination for application to other studies. This computational study will help select NGS-based BSA statistics that are useful to the broad scientific community. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08718-y.
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17
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Zhong L, Zhu Y, Olsen KM. Hard versus soft selective sweeps during domestication and improvement in soybean. Mol Ecol 2022; 31:3137-3153. [PMID: 35366022 DOI: 10.1111/mec.16454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/16/2022] [Accepted: 03/28/2022] [Indexed: 11/28/2022]
Abstract
Genome scans for selection can provide an efficient way to dissect the genetic basis of domestication traits and understand mechanisms of adaptation during crop evolution. Selection involving soft sweeps (simultaneous selection for multiple alleles) is probably common in plant genomes but is under-studied, and few if any studies have systematically scanned for soft sweeps in the context of crop domestication. Using genome resequencing data from 302 wild and domesticated soybean accessions, we conducted selection scans using five widely employed statistics to identify selection candidates under classical (hard) and soft sweeps. Across the genome, inferred hard sweeps are predominant in domesticated soybean landraces and improved varieties, whereas soft sweeps are more prevalent in a representative subpopulation of the wild ancestor. Six domestication-related genes, representing both hard and soft sweeps and different stages of domestication, were used as positive controls to assess the detectability of domestication-associated sweeps. Performance of various test statistics suggests that differentiation-based (FST ) methods are robust for detecting complete hard sweeps, and that LD-based strategies perform well for identifying recent/ongoing sweeps; however, none of the test statistics detected a known soft sweep we previously documented at the domestication gene Dt1. Genome scans yielded a set of 66 candidate loci that were identified by both differentiation-based and LD-based (iHH) methods; notably, this shared set overlaps with many previously identified QTLs for soybean domestication/improvement traits. Collectively, our results will help to advance genetic characterizations of soybean domestication traits and shed light on selection modes involved in adaptation in domesticated plant species.
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Affiliation(s)
- Limei Zhong
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi, School of Life Sciences, Nanchang University, Nanchang, China
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi, School of Life Sciences, Nanchang University, Nanchang, China
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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18
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Huang X, Huang S, Han B, Li J. The integrated genomics of crop domestication and breeding. Cell 2022; 185:2828-2839. [PMID: 35643084 DOI: 10.1016/j.cell.2022.04.036] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 12/13/2022]
Abstract
As a major event in human civilization, wild plants were successfully domesticated to be crops, largely owing to continuing artificial selection. Here, we summarize new discoveries made during the past decade in crop domestication and breeding. The construction of crop genome maps and the functional characterization of numerous trait genes provide foundational information. Approaches to read, interpret, and write complex genetic information are being leveraged in many plants for highly efficient de novo or re-domestication. Understanding the underlying mechanisms of crop microevolution and applying the knowledge to agricultural productions will give possible solutions for future challenges in food security.
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Affiliation(s)
- Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
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19
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Cui D, Zhou H, Ma X, Lin Z, Sun L, Han B, Li M, Sun J, Liu J, Jin G, Wang X, Cao G, Deng XW, He H, Han L. Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars. PLANT COMMUNICATIONS 2022; 3:100325. [PMID: 35576158 PMCID: PMC9251437 DOI: 10.1016/j.xplc.2022.100325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/12/2022] [Accepted: 04/09/2022] [Indexed: 06/15/2023]
Abstract
Hybridization between Xian/indica (XI) and Geng/japonica (GJ) rice combined with utilization of plant ideotypes has greatly contributed to yield improvements in modern GJ rice in China over the past 50 years. To explore the genomic basis of improved yield and disease resistance in GJ rice, we conducted a large-scale genomic landscape analysis of 816 elite GJ cultivars representing multiple eras of germplasm from China. We detected consistently increasing introgressions from three XI subpopulations into GJ cultivars since the 1980s and found that the XI genome introgressions significantly increased the grain number per panicle (GN) and decreased the panicle number per plant. This contributed to the improvement of plant type during modern breeding, changing multi-tiller plants to moderate tiller plants with a large panicle size and increasing the blast resistance. Notably, we found that key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1, SMG1, DEP3, Pib, Pi-d2, and Bph3, were introduced from XI rice by introgression. By GWAS analysis, we detected a GN-related gene Gnd5, which had been consistently introgressed from XI into GJ cultivars since the 1980s. Gnd5 is a GRAS transcription factor gene, and Gnd5 knockout mutants showed a significant reduction in GN. The estimated genetic effects of genes varied among different breeding locations, which explained the distinct introgression levels of XI gene haplotypes, including Gnd5, DEP3, etc., to these GJ breeding pedigrees. These findings reveal the genomic contributions of introgressions from XI to the trait improvements of GJ rice cultivars and provide new insights for future rice genomic breeding.
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Affiliation(s)
- Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Han Zhou
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zechuan Lin
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Linhua Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Maomao Li
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jianchang Sun
- Institute of Crop Research, Ningxia Academy of Agricultural and Forestry Sciences, Yongning 750105, China
| | - Jin Liu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Guixiu Jin
- Rice Research Institute, Linyi Academy of Agricultural Sciences, Shandong Linyi 276012, China
| | - Xianju Wang
- Rice Research Institute of Liaoning Province, Shenyang 110161, China
| | - Guilan Cao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China.
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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20
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Gutaker RM, Chater CCC, Brinton J, Castillo-Lorenzo E, Breman E, Pironon S. Scaling up neodomestication for climate-ready crops. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102169. [PMID: 35065528 DOI: 10.1016/j.pbi.2021.102169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/15/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
We can increase the stability of our food systems against environmental variability and climate change by following the footsteps of our ancestors and domesticating edible wild plants. Reinforced by recent advances in comparative genomics and gene editing technologies, neodomestication opens possibilities for a rapid generation of new crops. By starting the candidate selection pipeline with climatic parameters, we orient neodomestication efforts to increase food security against climate change. We highlight the fact that the edible species conservation and characterization will be key in this process. Utilization of genetic resources, entrusted to conservationists and researchers by local communities, has to be conducted with highest ethical standards and benefit-sharing in mind.
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Affiliation(s)
- Rafal M Gutaker
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey, TW9 3AE, UK.
| | - Caspar C C Chater
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey, TW9 3AE, UK
| | - Jemima Brinton
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey, TW9 3AE, UK
| | - Elena Castillo-Lorenzo
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath, West Sussex, RH17 6TN, UK
| | - Elinor Breman
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath, West Sussex, RH17 6TN, UK
| | - Samuel Pironon
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey, TW9 3AE, UK.
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21
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Circum-Saharan Prehistory through the Lens of mtDNA Diversity. Genes (Basel) 2022; 13:genes13030533. [PMID: 35328086 PMCID: PMC8951852 DOI: 10.3390/genes13030533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
African history has been significantly influenced by the Sahara, which has represented a barrier for migrations of all living beings, including humans. Major exceptions were the gene flow events that took place between North African and sub-Saharan populations during the so-called African Humid Periods, especially in the Early Holocene (11.5 to 5.5 thousand years ago), and more recently in connection with trans-Saharan commercial routes. In this study, we describe mitochondrial DNA (mtDNA) diversity of human populations from both sides of the Sahara Desert, i.e., both from North Africa and the Sahel/Savannah belt. The final dataset of 7213 mtDNA sequences from 134 African populations encompasses 470 newly collected and 6743 previously published samples, which were analyzed using descriptive methods and Bayesian statistics. We completely sequenced 26 mtDNAs from sub-Saharan samples belonging to the Eurasian haplogroup N1. Analyses of these N1 mitogenomes revealed their possible routes to the Sahel, mostly via Bab el-Mandab. Our results indicate that maternal gene flow must have been important in this circum-Saharan space, not only within North Africa and the Sahel/Savannah belt but also between these two regions.
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22
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Kulichová I, Mouterde M, Mokhtar MG, Diallo I, Tříska P, Diallo YM, Hofmanová Z, Poloni ES, Černý V. Demographic history was a formative mechanism of the genetic structure for the taste receptor TAS2R16 in human populations inhabiting Africa's Sahel/Savannah Belt. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 177:540-555. [PMID: 34846066 DOI: 10.1002/ajpa.24448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/05/2021] [Accepted: 11/03/2021] [Indexed: 11/12/2022]
Abstract
OBJECTIVES Mode of subsistence is an important factor influencing dietary habits and the genetic structure of various populations through differential intensity of gene flow and selection pressures. Previous studies suggest that in Africa Taste 2 Receptor Member 16 (TAS2R16), which encodes the 7-transmembrane receptor protein for bitterness, might also be under positive selection pressure. METHODS However, since sampling coverage of populations was limited, we created a new TAS2R16 population dataset from across the African Sahel/Savannah belt representing various local populations of differing subsistence modes, linguistic affiliations, and geographic provenience. We sequenced the TAS2R16 exon gene and analyzed 2250 haplotypes among 19 populations. RESULTS We found no evidence for selection as a driving force of genetic variation at this locus; instead, we discovered a highly significant correlation between TAS2R16 genetic and geographical distances based on provenience of the sampled populations, strongly suggesting that genetic drift most likely prevailed over positive selection at this specific locus. We also found significant correlations with other independent loci, mainly in sedentary farmers. DISCUSSION Our results do not support the notion that the genetic diversity of TAS2R16 in Sahelian populations was shaped by selective pressures. This could result from several alternative and not mutually exclusive mechanisms, of which the possibility that, due to the pleiotropic nature of TAS2R16, selective pressures on other traits could counterbalance those acting on bitter taste perception, or that the change of diet in the Neolithic generally relaxed selective pressure on this gene.
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Affiliation(s)
- Iva Kulichová
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Médéric Mouterde
- Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Mohammed G Mokhtar
- Arabic Department, Faculty of Arts, University of Kordofan, Al-Ubayyid, Sudan
| | - Issa Diallo
- Département de Linguistique et Langues Nationales, Institut des Sciences des Sociétés, CNRST, Ouagadougou, Burkina Faso
| | - Petr Tříska
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Yoro Mame Diallo
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Zuzana Hofmanová
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czech Republic
| | - Estella S Poloni
- Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
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23
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Lv Y, Ma J, Wei H, Xiao F, Wang Y, Jahan N, Hazman M, Qian Q, Shang L, Guo L. Combining GWAS, Genome-Wide Domestication and a Transcriptomic Analysis Reveals the Loci and Natural Alleles of Salt Tolerance in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:912637. [PMID: 35783926 PMCID: PMC9248812 DOI: 10.3389/fpls.2022.912637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/23/2022] [Indexed: 05/12/2023]
Abstract
Soil salinity poses a serious threat to the sustainable production of rice (Oryza sativa L.) throughout the world. Thus, the detection of loci and alleles responsible for salt tolerance is fundamental to accelerating the improvement of rice and producing the resilient varieties that will ensure future harvests. In this study, we collected a set of 191 mini-core rice populations from around the world, evaluated their salt tolerance based on plant growth and development phenotypes at the seedling stage, and divided a standard evaluation score (SES) of visual salt injury into five different grades. We used ∼3.82 million single nucleotide polymorphisms (SNPs) to identify 155 significant SNPs and 275 genes associated with salt sensitivity based on a genome-wide association study (GWAS) of SES. In particular, two candidate genes, ZFP179 and OsDSR2, were associated with salt tolerance, and OsHKT1;1 was co-detected in the entire GWAS of all the panels and indica. Additionally, we investigated the transcriptional changes in cultivars 93-11 and PA64s under normal and salinity stress conditions and found 517 co-upregulated and 223 co-downregulated genes. These differentially expressed genes (DEGs) were highly enriched in "response to chemical" and "stress" based on the gene ontology enrichment analysis. Notably, 30 candidate genes that were associated with the salt tolerance analysis were obtained by integrating GWAS and transcriptomic DEG analyses, including 13 cloned genes that had no reports of tolerance to salt and 17 candidate genes whose functions were unknown. To further explore these genes and their alleles, we performed haplotype analysis, genome-wide domestication detection, and transcriptome analysis to breed improved varieties. This data and the genetic resources provided will be valuable for the development of salt tolerant rice varieties.
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Affiliation(s)
- Yang Lv
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jie Ma
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hua Wei
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fang Xiao
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yueying Wang
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Noushin Jahan
- Department of Agronomy, Khulna Agricultural University, Khulna, Bangladesh
| | - Mohamed Hazman
- Agricultural Genetic Engineering Research Institute, Giza, Egypt
| | - Qian Qian
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Lianguang Shang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Longbiao Guo,
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Longbiao Guo,
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24
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Burban E, Tenaillon MI, Le Rouzic A. Gene network simulations provide testable predictions for the molecular domestication syndrome. Genetics 2021; 220:6440055. [PMID: 34849852 DOI: 10.1093/genetics/iyab214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/15/2021] [Indexed: 11/14/2022] Open
Abstract
The domestication of plant species lead to repeatable morphological evolution, often referred to as the phenotypic domestication syndrome. Domestication is also associated with important genomic changes, such as the loss of genetic diversity compared to adequately large wild populations, and modifications of gene expression patterns. Here, we explored theoretically the effect of a domestication-like scenario on the evolution of gene regulatory networks. We ran population genetics simulations in which individuals were featured by their genotype (an interaction matrix encoding a gene regulatory network) and their gene expressions, representing the phenotypic level. Our domestication scenario included a population bottleneck and a selection switch mimicking human-mediated directional and canalizing selection, i.e., change in the optimal gene expression level and selection towards more stable expression across environments. We showed that domestication profoundly alters genetic architectures. Based on four examples of plant domestication scenarios, our simulations predict (i) a drop in neutral allelic diversity, (ii) a change in gene expression variance that depends upon the domestication scenario, (iii) transient maladaptive plasticity, (iv) a deep rewiring of the gene regulatory networks, with a trend towards gain of regulatory interactions, and (v) a global increase in the genetic correlations among gene expressions, with a loss of modularity in the resulting coexpression patterns and in the underlying networks. We provide empirically testable predictions on the differences of genetic architectures between wild and domesticated forms. The characterization of such systematic evolutionary changes in the genetic architecture of traits contributes to define a molecular domestication syndrome.
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Affiliation(s)
- Ewen Burban
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France.,CNRS, Univ. Rennes, ECOBIO-UMR 6553, F-35000 Rennes, France
| | - Maud I Tenaillon
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190, Gif-sur-Yvette, France
| | - Arnaud Le Rouzic
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
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25
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Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication. Int J Mol Sci 2021; 22:ijms22147578. [PMID: 34299195 PMCID: PMC8305476 DOI: 10.3390/ijms22147578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/29/2021] [Accepted: 07/08/2021] [Indexed: 01/25/2023] Open
Abstract
Betaine aldehyde dehydrogenase 1 (BADH1), a paralog of the fragrance gene BADH2, is known to be associated with salt stress through the accumulation of synthesized glycine betaine (GB), which is involved in the response to abiotic stresses. Despite the unclear association between BADH1 and salt stress, we observed the responses of eight phenotypic characteristics (germination percentage (GP), germination energy (GE), germination index (GI), mean germination time (MGT), germination rate (GR), shoot length (SL), root length (RL), and total dry weight (TDW)) to salt stress during the germination stage of 475 rice accessions to investigate their association with BADH1 haplotypes. We found a total of 116 SNPs and 77 InDels in the whole BADH1 gene region, representing 39 haplotypes. Twenty-nine haplotypes representing 27 mutated alleles (two InDels and 25 SNPs) were highly (p < 0.05) associated with salt stress, including the five SNPs that have been previously reported to be associated with salt tolerance. We observed three predominant haplotypes associated with salt tolerance, Hap_2, Hap_18, and Hap_23, which were Indica specific, indicating a comparatively high number of rice accessions among the associated haplotypes. Eight plant parameters (phenotypes) also showed clear responses to salt stress, and except for MGT (mean germination time), all were positively correlated with each other. Different signatures of domestication for BADH1 were detected in cultivated rice by identifying the highest and lowest Tajima’s D values of two major cultivated ecotypes (Temperate Japonica and Indica). Our findings on these significant associations and BADH1 evolution to plant traits can be useful for future research development related to its gene expression.
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26
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Pérez-Escobar OA, Bellot S, Przelomska NAS, Flowers JM, Nesbitt M, Ryan P, Gutaker RM, Gros-Balthazard M, Wells T, Kuhnhäuser BG, Schley R, Bogarín D, Dodsworth S, Diaz R, Lehmann M, Petoe P, Eiserhardt WL, Preick M, Hofreiter M, Hajdas I, Purugganan M, Antonelli A, Gravendeel B, Leitch IJ, Torres Jimenez MF, Papadopulos AST, Chomicki G, Renner SS, Baker WJ. Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication. Mol Biol Evol 2021; 38:4475-4492. [PMID: 34191029 PMCID: PMC8476131 DOI: 10.1093/molbev/msab188] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.
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Affiliation(s)
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jonathan M Flowers
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Mark Nesbitt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Philippa Ryan
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Muriel Gros-Balthazard
- French National Research Institute for Sustainable Development, Montpellier, BP 64501 - 34394 Cedex 5, France
| | - Tom Wells
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Rowan Schley
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Diego Bogarín
- Lankester Botanical Garden, University of Costa Rica, San José, 302-7050, Costa Rica
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Rudy Diaz
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Peter Petoe
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Michaela Preick
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Michael Hofreiter
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Irka Hajdas
- Department of Earth Sciences, ETH Zurich, 8092, Switzerland
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK.,Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | | | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Maria Fernanda Torres Jimenez
- Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | - Alexander S T Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, University of Bangor, Bangor LL57 2UW, UK
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
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27
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Bourgeois YXC, Warren BH. An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes. Mol Ecol 2021; 30:6036-6071. [PMID: 34009688 DOI: 10.1111/mec.15989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.
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Affiliation(s)
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP 51, Paris, France
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28
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Shen QK, Peng MS, Adeola AC, Kui L, Duan S, Miao YW, Eltayeb NM, Lichoti JK, Otecko NO, Strillacci MG, Gorla E, Bagnato A, Charles OS, Sanke OJ, Dawuda PM, Okeyoyin AO, Musina J, Njoroge P, Agwanda B, Kusza S, Nanaei HA, Pedar R, Xu MM, Du Y, Nneji LM, Murphy RW, Wang MS, Esmailizadeh A, Dong Y, Ommeh SC, Zhang YP. Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa. Genome Biol Evol 2021; 13:6261762. [PMID: 34009300 PMCID: PMC8214406 DOI: 10.1093/gbe/evab090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 12/22/2022] Open
Abstract
Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.
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Affiliation(s)
- Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Ling Kui
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Yong-Wang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Nada M Eltayeb
- Department of Animal breeding and Reproduction Technology, College of Animal Production, University of Bahri, Khartoum, Sudan
| | - Jacqueline K Lichoti
- State Department of Livestock, Ministry of Agriculture Livestock Fisheries and Irrigation, Nairobi, Kenya
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | | | - Erica Gorla
- Department of Veterinary Medicine, Università degli Studi di Milano, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Italy
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture, Makurdi, Nigeria
| | - Agboola O Okeyoyin
- National Park Service Headquarter, Federal Capital Territory, Abuja, Nigeria
| | - John Musina
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Peter Njoroge
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, Hungary
| | | | - Rana Pedar
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran
| | - Ming-Min Xu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yuan Du
- Nowbio Biotechnology Company, Kunming, China
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, California, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, California, USA
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran
| | - Yang Dong
- College of Biological Big Data, Yunnan Agriculture University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Sheila C Ommeh
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya.,Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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29
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Wang P, Zhou G, Jian J, Yang H, Renshaw D, Aubert MK, Clements J, He T, Sweetingham M, Li C. Whole-genome assembly and resequencing reveal genomic imprint and key genes of rapid domestication in narrow-leafed lupin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1192-1210. [PMID: 33249667 DOI: 10.1111/tpj.15100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/17/2020] [Accepted: 11/20/2020] [Indexed: 05/04/2023]
Abstract
Shifting from a livestock-based protein diet to a plant-based protein diet has been proposed as an essential requirement to maintain global food sustainability, which requires the increased production of protein-rich crops for direct human consumption. Meanwhile, the lack of sufficient genetic diversity in crop varieties is an increasing concern for sustainable food supplies. Countering this concern requires a clear understanding of the domestication process and dynamics. Narrow-leafed lupin (Lupinus angustifolius L.) has experienced rapid domestication and has become a new legume crop over the past century, with the potential to provide protein-rich seeds. Here, using long-read whole-genome sequencing, we assembled the third-generation reference genome for the narrow-leafed lupin cultivar Tanjil, comprising 20 chromosomes with a total genome size of 615.8 Mb and contig N50 = 5.65 Mb. We characterized the original mutation and putative biological pathway resulting in low seed alkaloid level that initiated the recent domestication of narrow-leafed lupin. We identified a 1133-bp insertion in the cis-regulatory region of a putative gene that may be associated with reduced pod shattering (lentus). A comparative analysis of genomic diversity in cultivars and wild types identified an apparent domestication bottleneck, as precisely predicted by the original model of the bottleneck effect on genetic variability in populations. Our results identify the key domestication genetic loci and provide direct genomic evidence for a domestication bottleneck, and open up the possibility of knowledge-driven de novo domestication of wild plants as an avenue to broaden crop plant diversity to enhance food security and sustainable low-carbon emission agriculture.
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Affiliation(s)
- Penghao Wang
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia
- Western Crop Genetics Alliance, Western Australian Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Gaofeng Zhou
- Western Crop Genetics Alliance, Western Australian Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Department of Primary Industries and Regional Development, Government of Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huaan Yang
- Department of Primary Industries and Regional Development, Government of Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Daniel Renshaw
- Department of Primary Industries and Regional Development, Government of Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Matthew K Aubert
- Australian Grain Technologies Pty Ltd, 100 Byfield Street, Northam, WA, 6041, Australia
| | - Jonathan Clements
- Green Blueprint Pty Ltd, 117C Hastings Street, Scarborough, WA, 6019, Australia
- Glycemic Lupin Company Pty Ltd, 33 Commercial St, Coorow, WA, 6515, Australia
| | - Tianhua He
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia
- Western Crop Genetics Alliance, Western Australian Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Mark Sweetingham
- Department of Primary Industries and Regional Development, Government of Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Chengdao Li
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia
- Western Crop Genetics Alliance, Western Australian Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Department of Primary Industries and Regional Development, Government of Western Australia, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
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30
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Wambugu PW, Ndjiondjop MN, Henry R. Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication. RICE (NEW YORK, N.Y.) 2021; 14:6. [PMID: 33415579 PMCID: PMC7790969 DOI: 10.1186/s12284-020-00449-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.
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Affiliation(s)
- Peterson W. Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, Nairobi, 00100 Kenya
| | - Marie-Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551 Bouaké 01, Côte d’Ivoire
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
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31
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Kim MS, Lozano R, Kim JH, Bae DN, Kim ST, Park JH, Choi MS, Kim J, Ok HC, Park SK, Gore MA, Moon JK, Jeong SC. The patterns of deleterious mutations during the domestication of soybean. Nat Commun 2021; 12:97. [PMID: 33397978 PMCID: PMC7782591 DOI: 10.1038/s41467-020-20337-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
Globally, soybean is a major protein and oil crop. Enhancing our understanding of the soybean domestication and improvement process helps boost genomics-assisted breeding efforts. Here we present a genome-wide variation map of 10.6 million single-nucleotide polymorphisms and 1.4 million indels for 781 soybean individuals which includes 418 domesticated (Glycine max), 345 wild (Glycine soja), and 18 natural hybrid (G. max/G. soja) accessions. We describe the enhanced detection of 183 domestication-selective sweeps and the patterns of putative deleterious mutations during domestication and improvement. This predominantly selfing species shows 7.1% reduction of overall deleterious mutations in domesticated soybean relative to wild soybean and a further 1.4% reduction from landrace to improved accessions. The detected domestication-selective sweeps also show reduced levels of deleterious alleles. Importantly, genotype imputation with this resource increases the mapping resolution of genome-wide association studies for seed protein and oil traits in a soybean diversity panel.
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Affiliation(s)
- Myung-Shin Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
- Plant Immunity Research Center, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Ji Hong Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
| | - Dong Nyuk Bae
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
| | - Sang-Tae Kim
- Department of Life Science, The Catholic University of Korea, Bucheon, 14662, Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
| | - Man Soo Choi
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Jaehyun Kim
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Hyun-Choong Ok
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Soo-Kwon Park
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Jung-Kyung Moon
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea.
- Agricultural Genome Center, National Academy of Agricultural Sciences, Rural Development Administration, Jeonju, Jeonbuk, 55365, Korea.
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea.
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32
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Chen Q, Li W, Tan L, Tian F. Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding. MOLECULAR PLANT 2021; 14:9-26. [PMID: 33316465 DOI: 10.1016/j.molp.2020.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 05/11/2023]
Abstract
Crop domestication has fundamentally altered the course of human history, causing a shift from hunter-gatherer to agricultural societies and stimulating the rise of modern civilization. A greater understanding of crop domestication would provide a theoretical basis for how we could improve current crops and develop new crops to deal with environmental challenges in a sustainable manner. Here, we provide a comprehensive summary of the similarities and differences in the domestication processes of maize and rice, two major staple food crops that feed the world. We propose that maize and rice might have evolved distinct genetic solutions toward domestication. Maize and rice domestication appears to be associated with distinct regulatory and evolutionary mechanisms. Rice domestication tended to select de novo, loss-of-function, coding variation, while maize domestication more frequently favored standing, gain-of-function, regulatory variation. At the gene network level, distinct genetic paths were used to acquire convergent phenotypes in maize and rice domestication, during which different central genes were utilized, orthologous genes played different evolutionary roles, and unique genes or regulatory modules were acquired for establishing new traits. Finally, we discuss how the knowledge gained from past domestication processes, together with emerging technologies, could be exploited to improve modern crop breeding and domesticate new crops to meet increasing human demands.
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Affiliation(s)
- Qiuyue Chen
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Weiya Li
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lubin Tan
- State Key Laboratory of Agrobiotechnology, National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China.
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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33
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Leroy T, Rougemont Q. Introduction to Population Genomics Methods. Methods Mol Biol 2021; 2222:287-324. [PMID: 33301100 DOI: 10.1007/978-1-0716-0997-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-throughput sequencing technologies have provided an unprecedented opportunity to study the different evolutionary forces that have shaped present-day patterns of genetic diversity, with important implications for many directions in plant biology research. To manage such massive quantities of sequencing data, biologists, however, need new additional skills in informatics and statistics. In this chapter, our objective is to introduce population genomics methods to beginners following a learning-by-doing strategy in order to help the reader to analyze the sequencing data by themselves. Conducted analyses cover several main areas of evolutionary biology, such as an initial description of the evolutionary history of a given species or the identification of genes targeted by natural or artificial selection. In addition to the practical advices, we performed re-analyses of two cases studies with different kind of data: a domesticated cereal (African rice) and a non-domesticated tree species (sessile oak). All the code needed to replicate this work is publicly available on github ( https://github.com/ThibaultLeroyFr/Intro2PopGenomics/ ).
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Affiliation(s)
- Thibault Leroy
- Montpellier Institute of Evolutionary Sciences (ISEM), Université de Montpellier, Montpellier, France. .,Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
| | - Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, QC, Canada
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34
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Arnoux S, Fraïsse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. J Evol Biol 2020; 34:270-283. [PMID: 33107098 DOI: 10.1111/jeb.13723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/15/2020] [Indexed: 12/30/2022]
Abstract
Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a "protracted period" of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.
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Affiliation(s)
- Stéphanie Arnoux
- INRA UR1052 GAFL, Centre de Recherche INRA PACA, Avignon Cedex 9, France.,Vilmorin SA, Lédenon, France
| | | | - Christopher Sauvage
- INRA UR1052 GAFL, Centre de Recherche INRA PACA, Avignon Cedex 9, France.,Syngenta SAS France, Saint Sauveur, France
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35
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Černý V, Fortes-Lima C, Tříska P. Demographic history and admixture dynamics in African Sahelian populations. Hum Mol Genet 2020; 30:R29-R36. [PMID: 33105478 DOI: 10.1093/hmg/ddaa239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/18/2023] Open
Abstract
The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterized by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure and the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.
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Affiliation(s)
- Viktor Černý
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Cesar Fortes-Lima
- Subdepartment of Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Petr Tříska
- Archaeogenetics Laboratory, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
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36
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Cubry P, Pidon H, Ta KN, Tranchant-Dubreuil C, Thuillet AC, Holzinger M, Adam H, Kam H, Chrestin H, Ghesquière A, François O, Sabot F, Vigouroux Y, Albar L, Jouannic S. Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima. RICE (NEW YORK, N.Y.) 2020; 13:66. [PMID: 32936396 PMCID: PMC7494698 DOI: 10.1186/s12284-020-00424-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/31/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species. RESULTS Using a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we found several association peaks, one of which co-localised with a well described gene in the Asian rice flowering pathway, OsGi, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting genomic regions and candidate genes. Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations. CONCLUSION Our results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.
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Affiliation(s)
| | - Hélène Pidon
- DIADE, Univ Montpellier, IRD, Montpellier, France
- Present address: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Kim Nhung Ta
- LMI RICE, AGI, IRD, Univ Montpellier, CIRAD, USTH, Hanoi, Vietnam
- Present address: National Institute of Genetics, Mishima, Shizuoka, Japan
| | | | | | | | - Hélène Adam
- DIADE, Univ Montpellier, IRD, Montpellier, France
| | | | | | | | - Olivier François
- Université Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble, France
| | | | | | | | - Stefan Jouannic
- DIADE, Univ Montpellier, IRD, Montpellier, France.
- LMI RICE, AGI, IRD, Univ Montpellier, CIRAD, USTH, Hanoi, Vietnam.
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Abrouk M, Ahmed HI, Cubry P, Šimoníková D, Cauet S, Pailles Y, Bettgenhaeuser J, Gapa L, Scarcelli N, Couderc M, Zekraoui L, Kathiresan N, Čížková J, Hřibová E, Doležel J, Arribat S, Bergès H, Wieringa JJ, Gueye M, Kane NA, Leclerc C, Causse S, Vancoppenolle S, Billot C, Wicker T, Vigouroux Y, Barnaud A, Krattinger SG. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nat Commun 2020; 11:4488. [PMID: 32901040 PMCID: PMC7479619 DOI: 10.1038/s41467-020-18329-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/16/2020] [Indexed: 01/24/2023] Open
Abstract
Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.
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Affiliation(s)
- Michael Abrouk
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Hanin Ibrahim Ahmed
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Denisa Šimoníková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Yveline Pailles
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jan Bettgenhaeuser
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Liubov Gapa
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | | | - Nagarajan Kathiresan
- Supercomputing Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Hélène Bergès
- CNRGV Plant Genomics Center, INRAE, Toulouse, France
- Inari Agriculture, One Kendall Square Building 600/700, Cambridge, MA, 02139, USA
| | | | - Mathieu Gueye
- Laboratoire de Botanique, Département de Botanique et Géologie, IFAN Ch. A. Diop/UCAD, Dakar, Senegal
| | - Ndjido A Kane
- Senegalese Agricultural Research Institute, Dakar, Senegal
- Laboratoire Mixte International LAPSE, Dakar, Senegal
| | - Christian Leclerc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Sandrine Causse
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Sylvie Vancoppenolle
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Claire Billot
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
| | | | - Adeline Barnaud
- DIADE, Univ Montpellier, IRD, Montpellier, France.
- Laboratoire Mixte International LAPSE, Dakar, Senegal.
| | - Simon G Krattinger
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Abrouk M, Ahmed HI, Cubry P, Šimoníková D, Cauet S, Pailles Y, Bettgenhaeuser J, Gapa L, Scarcelli N, Couderc M, Zekraoui L, Kathiresan N, Čížková J, Hřibová E, Doležel J, Arribat S, Bergès H, Wieringa JJ, Gueye M, Kane NA, Leclerc C, Causse S, Vancoppenolle S, Billot C, Wicker T, Vigouroux Y, Barnaud A, Krattinger SG. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nat Commun 2020; 11:4488. [PMID: 32901040 DOI: 10.1101/2020.04.11.037671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/16/2020] [Indexed: 05/28/2023] Open
Abstract
Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.
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Affiliation(s)
- Michael Abrouk
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Hanin Ibrahim Ahmed
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Denisa Šimoníková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Yveline Pailles
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jan Bettgenhaeuser
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Liubov Gapa
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | | | - Nagarajan Kathiresan
- Supercomputing Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Hélène Bergès
- CNRGV Plant Genomics Center, INRAE, Toulouse, France
- Inari Agriculture, One Kendall Square Building 600/700, Cambridge, MA, 02139, USA
| | | | - Mathieu Gueye
- Laboratoire de Botanique, Département de Botanique et Géologie, IFAN Ch. A. Diop/UCAD, Dakar, Senegal
| | - Ndjido A Kane
- Senegalese Agricultural Research Institute, Dakar, Senegal
- Laboratoire Mixte International LAPSE, Dakar, Senegal
| | - Christian Leclerc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Sandrine Causse
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Sylvie Vancoppenolle
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Claire Billot
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
| | | | - Adeline Barnaud
- DIADE, Univ Montpellier, IRD, Montpellier, France.
- Laboratoire Mixte International LAPSE, Dakar, Senegal.
| | - Simon G Krattinger
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Hamzelou S, Kamath KS, Masoomi-Aladizgeh F, Johnsen MM, Atwell BJ, Haynes PA. Wild and Cultivated Species of Rice Have Distinctive Proteomic Responses to Drought. Int J Mol Sci 2020; 21:ijms21175980. [PMID: 32825202 PMCID: PMC7504292 DOI: 10.3390/ijms21175980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 12/25/2022] Open
Abstract
Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species (Oryza sativa cv. Nipponbare and Oryza glaberrima cv. CG14) and an endemic, perennial Australian wild species (Oryza australiensis) were grown in soil at 40% field capacity for 7 d (drought). The hypothesis was that the natural tolerance of O. australiensis to erratic water supply would be reflected in a unique proteomic profile. Leaves from droughted plants and well-watered controls were harvested for label-free quantitative shotgun proteomics. Physiological and gene ontology analysis confirmed that O. australiensis responded uniquely to drought, with superior leaf water status and enhanced levels of photosynthetic proteins. Distinctive patterns of protein accumulation in drought were observed across the O. australiensis proteome. Photosynthetic and stress-response proteins were more abundant in drought-affected O. glaberrima than O. sativa, and were further enriched in O. australiensis. In contrast, the level of accumulation of photosynthetic proteins decreased when O. sativa underwent drought, while a narrower range of stress-responsive proteins showed increased levels of accumulation. Distinctive proteomic profiles and the accumulated levels of individual proteins with specific functions in response to drought in O. australiensis indicate the importance of this species as a source of stress tolerance genes.
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Affiliation(s)
- Sara Hamzelou
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
| | - Karthik Shantharam Kamath
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Farhad Masoomi-Aladizgeh
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (F.M.-A.); (B.J.A.)
| | - Matthew M. Johnsen
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
| | - Brian J. Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (F.M.-A.); (B.J.A.)
| | - Paul A. Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
- Correspondence:
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40
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Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing. Sci Rep 2020; 10:13995. [PMID: 32814806 PMCID: PMC7438528 DOI: 10.1038/s41598-020-70842-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022] Open
Abstract
To minimize the cost of sample preparation and genotyping, most genebank genomics studies in self-pollinating species are conducted on a single individual to represent an accession, which may be heterogeneous with larger than expected intra-accession genetic variation. Here, we compared various population genetics parameters among six DNA (leaf) sampling methods on 90 accessions representing a wild species (O. barthii), cultivated and landraces (O. glaberrima, O. sativa), and improved varieties derived through interspecific hybridizations. A total of 1,527 DNA samples were genotyped with 46,818 polymorphic single nucleotide polymorphisms (SNPs) using DArTseq. Various statistical analyses were performed on eleven datasets corresponding to 5 plants per accession individually and in a bulk (two sets), 10 plants individually and in a bulk (two sets), all 15 plants individually (one set), and a randomly sampled individual repeated six times (six sets). Overall, we arrived at broadly similar conclusions across 11 datasets in terms of SNP polymorphism, heterozygosity/heterogeneity, diversity indices, concordance among genetic dissimilarity matrices, population structure, and genetic differentiation; there were, however, a few discrepancies between some pairs of datasets. Detailed results of each sampling method, the concordance in their outputs, and the technical and cost implications of each method were discussed.
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Abstract
Domestication is a co-evolutionary process that occurs when wild plants are brought into cultivation by humans, leading to origin of new species and/or differentiated populations that are critical for human survival. Darwin used domesticated species as early models for evolution, highlighting their variation and the key role of selection in species differentiation. Over the last two decades, a growing synthesis of plant genetics, genomics, and archaeobotany has led to challenges to old orthodoxies and the advent of fresh perspectives on how crop domestication and diversification proceed. I discuss four new insights into plant domestication - that in general domestication is a protracted process, that unconscious (natural) selection plays a prominent role, that interspecific hybridization may be an important mechanism for crop species diversification and range expansion, and that similar genes across multiple species underlies parallel/convergent phenotypic evolution between domesticated taxa. Insights into the evolutionary origin and diversification of crop species can help us in developing new varieties (and possibly even new species) to deal with current and future environmental challenges in a sustainable manner.
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Affiliation(s)
- Michael D Purugganan
- Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place New York University, New York, NY, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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Pidon H, Chéron S, Ghesquière A, Albar L. Allele mining unlocks the identification of RYMV resistance genes and alleles in African cultivated rice. BMC PLANT BIOLOGY 2020; 20:222. [PMID: 32429875 PMCID: PMC7236528 DOI: 10.1186/s12870-020-02433-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/07/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Rice yellow mottle virus (RYMV) is a major rice pathogen in Africa. Three resistance genes, i.e. RYMV1, RYMV2 and RYMV3, have been previously described. RYMV1 encodes the translation initiation factor eIF(iso)4G1 and the best candidate genes for RYMV2 and RYMV3 encode a homolog of an Arabidopsis nucleoporin (CPR5) and a nucleotide-binding domain and leucine-rich repeat containing domain (NLR) protein, respectively. High resistance is very uncommon in Asian cultivated rice (Oryza sativa), with only two highly resistant accessions identified so far, but it is more frequent in African cultivated rice (Oryza glaberrima). RESULTS Here we report the findings of a resistance survey in a reference collection of 268 O. glaberrima accessions. A total of 40 resistant accessions were found, thus confirming the high frequency of resistance to RYMV in this species. We analysed the variability of resistance genes or candidate genes in this collection based on high-depth Illumina data or Sanger sequencing. Alleles previously shown to be associated with resistance were observed in 31 resistant accessions but not in any susceptible ones. Five original alleles with a frameshift or untimely stop codon in the candidate gene for RYMV2 were also identified in resistant accessions. A genetic analysis revealed that these alleles, as well as T-DNA insertions in the candidate gene, were responsible of RYMV resistance. All 40 resistant accessions were ultimately linked to a validated or candidate resistance allele at one of the three resistance genes to RYMV. CONCLUSION This study demonstrated that the RYMV2 resistance gene is homologous to the Arabidopsis CPR5 gene and revealed five new resistance alleles at this locus. It also confirmed the close association between resistance and an amino-acid substitution in the leucine-rich repeat of the NLR candidate for RYMV3. We also provide an extensive overview of the genetic diversity of resistance to RYMV in the O. glaberrima species, while underlining the contrasted pattern of diversity between O. glaberrima and O. sativa for this trait. The different resistance genes and alleles will be instrumental in breeding varieties with sustainable field resistance to RYMV.
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Affiliation(s)
- Hélène Pidon
- DIADE, Univ. Montpellier, IRD, Montpellier, France
- Present Address: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
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Mao L, Chen M, Chu Q, Jia L, Sultana MH, Wu D, Kong X, Qiu J, Ye CY, Zhu QH, Chen X, Fan L. RiceRelativesGD: a genomic database of rice relatives for rice research. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5574892. [PMID: 31560050 PMCID: PMC6764101 DOI: 10.1093/database/baz110] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/25/2019] [Accepted: 08/09/2019] [Indexed: 12/02/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops worldwide. Its relatives, including phylogenetically related species of rice and paddy weeds with a similar ecological niche, can provide crucial genetic resources (such as resistance to biotic and abiotic stresses and high photosynthetic efficiency) for rice research. Although many rice genomic databases have been constructed, a database providing large-scale curated genomic data from rice relatives and offering specific gene resources is still lacking. Here, we present RiceRelativesGD, a user-friendly genomic database of rice relatives. RiceRelativesGD integrates large-scale genomic resources from 2 cultivated rice and 11 rice relatives, including 208 321 specific genes and 13 643 genes related to photosynthesis and responsive to external stimuli. Diverse bioinformatics tools are embedded in the database, which allow users to search, visualize and download the information of interest. To our knowledge, this is the first genomic database providing a centralized genetic resource of rice relatives. RiceRelativesGD will serve as a significant and comprehensive knowledgebase for the rice community.
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Affiliation(s)
- Lingfeng Mao
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
| | - Meihong Chen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Qinjie Chu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Lei Jia
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
| | - Most Humaira Sultana
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Dongya Wu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Xiangdong Kong
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Jie Qiu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Xi Chen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
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Lacchini E, Kiegle E, Castellani M, Adam H, Jouannic S, Gregis V, Kater MM. CRISPR-mediated accelerated domestication of African rice landraces. PLoS One 2020; 15:e0229782. [PMID: 32126126 PMCID: PMC7053755 DOI: 10.1371/journal.pone.0229782] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/13/2020] [Indexed: 11/18/2022] Open
Abstract
African Oryza glaberrima and Oryza sativa landraces are considered valuable resources for breeding traits due to their adaptation to local environmental and soil conditions. They often possess superior resistance to endemic pests and tolerance to drought and nutrient deficiencies when compared to the "imported" high production Asian rice varieties. In contrast, "domestication traits" such as seed shattering, lodging, and seed yield are not well established in these African landraces. Therefore, the use of these African varieties for high production agriculture is limited by unpredictable yield and grain quality. We are addressing this shortcoming by developing protocols for genetically transforming African landraces to allow the use of CRISPR-Cas mediated breeding approaches. Here we use as proof of concept the cultivated African landrace Kabre to target selected known "domestication loci" and improve the agronomic potential of Kabre rice. Stable genetic transformation with CRISPR-Cas9-based vectors generated single and simultaneous multiple gene knockouts. Plants with reduced stature to diminish lodging were generated by disrupting the HTD1 gene. Furthermore, three loci shown to control seed size and/or yield (GS3, GW2 and GN1A) were targeted using a multiplex CRISPR-Cas9 construct. This resulted in mutants with significantly improved seed yield. Our study provides an example of how new breeding technologies can accelerate the development of highly productive African landrace rice varieties, an important advancement considering that Africa is a hotspot for worldwide population growth and therefore prone to food shortage.
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Affiliation(s)
- Elia Lacchini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Edward Kiegle
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Hélène Adam
- University of Montpellier, DIADE, IRD, Montpellier, France
| | | | - Veronica Gregis
- Department of Biosciences, University of Milan, Milan, Italy
| | - Martin M. Kater
- Department of Biosciences, University of Milan, Milan, Italy
- * E-mail:
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Sempéré G, Pétel A, Rouard M, Frouin J, Hueber Y, De Bellis F, Larmande P. Gigwa v2-Extended and improved genotype investigator. Gigascience 2019; 8:5488103. [PMID: 31077313 PMCID: PMC6511067 DOI: 10.1093/gigascience/giz051] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/19/2019] [Accepted: 04/08/2019] [Indexed: 11/19/2022] Open
Abstract
Background The study of genetic variations is the basis of many research domains in biology. From genome structure to population dynamics, many applications involve the use of genetic variants. The advent of next-generation sequencing technologies led to such a flood of data that the daily work of scientists is often more focused on data management than data analysis. This mass of genotyping data poses several computational challenges in terms of storage, search, sharing, analysis, and visualization. While existing tools try to solve these challenges, few of them offer a comprehensive and scalable solution. Results Gigwa v2 is an easy-to-use, species-agnostic web application for managing and exploring high-density genotyping data. It can handle multiple databases and may be installed on a local computer or deployed as an online data portal. It supports various standard import and export formats, provides advanced filtering options, and offers means to visualize density charts or push selected data into various stand-alone or online tools. It implements 2 standard RESTful application programming interfaces, GA4GH, which is health-oriented, and BrAPI, which is breeding-oriented, thus offering wide possibilities of interaction with third-party applications. The project home page provides a list of live instances allowing users to test the system on public data (or reasonably sized user-provided data). Conclusions This new version of Gigwa provides a more intuitive and more powerful way to explore large amounts of genotyping data by offering a scalable solution to search for genotype patterns, functional annotations, or more complex filtering. Furthermore, its user-friendliness and interoperability make it widely accessible to the life science community.
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Affiliation(s)
- Guilhem Sempéré
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR INTERTRYP, F-34398 Montpellier, France.,South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,INTERTRYP, Univ Montpellier, CIRAD, Institut de Recherche pour le Développpement (IRD), Montpellier, France
| | - Adrien Pétel
- South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,DIADE, Univ Montpellier, IRD, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Mathieu Rouard
- South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Julien Frouin
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Institut national d'études supérieures agronomiques de Montpellier (Montpellier SupAgro), Montpellier, France
| | - Yann Hueber
- South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Fabien De Bellis
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Institut national d'études supérieures agronomiques de Montpellier (Montpellier SupAgro), Montpellier, France
| | - Pierre Larmande
- South Green Bioinformatics Platform, Bioversity, CIRAD, Institut National de la Recherche Agronomique (INRA), IRD, Montpellier, France.,DIADE, Univ Montpellier, IRD, 911 Avenue Agropolis, 34394 Montpellier, France
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Stetter MG, Vidal-Villarejo M, Schmid KJ. Parallel Seed Color Adaptation during Multiple Domestication Attempts of an Ancient New World Grain. Mol Biol Evol 2019; 37:1407-1419. [DOI: 10.1093/molbev/msz304] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AbstractThousands of plants have been selected as crops; yet, only a few are fully domesticated. The lack of adaptation to agroecological environments of many crop plants with few characteristic domestication traits potentially has genetic causes. Here, we investigate the incomplete domestication of an ancient grain from the Americas, amaranth. Although three grain amaranth species have been cultivated as crop for millennia, all three lack key domestication traits. We sequenced 121 crop and wild individuals to investigate the genomic signature of repeated incomplete adaptation. Our analysis shows that grain amaranth has been domesticated three times from a single wild ancestor. One trait that has been selected during domestication in all three grain species is the seed color, which changed from dark seeds to white seeds. We were able to map the genetic control of the seed color adaptation to two genomic regions on chromosomes 3 and 9, employing three independent mapping populations. Within the locus on chromosome 9, we identify an MYB-like transcription factor gene, a known regulator for seed color variation in other plant species. We identify a soft selective sweep in this genomic region in one of the crop species but not in the other two species. The demographic analysis of wild and domesticated amaranths revealed a population bottleneck predating the domestication of grain amaranth. Our results indicate that a reduced level of ancestral genetic variation did not prevent the selection of traits with a simple genetic architecture but may have limited the adaptation of complex domestication traits.
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Affiliation(s)
- Markus G Stetter
- Botanical Institute, University of Cologne, Cologne, Germany
- Department of Plant Breeding, Population Genetics and Seed Science, University of Hohenheim, Stuttgart, Germany
| | - Mireia Vidal-Villarejo
- Department of Plant Breeding, Population Genetics and Seed Science, University of Hohenheim, Stuttgart, Germany
| | - Karl J Schmid
- Department of Plant Breeding, Population Genetics and Seed Science, University of Hohenheim, Stuttgart, Germany
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Harrop TWR, Mantegazza O, Luong AM, Béthune K, Lorieux M, Jouannic S, Adam H. A set of AP2-like genes is associated with inflorescence branching and architecture in domesticated rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5617-5629. [PMID: 31346594 PMCID: PMC6812710 DOI: 10.1093/jxb/erz340] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/15/2019] [Indexed: 05/25/2023]
Abstract
Rice yield is influenced by inflorescence size and architecture, and inflorescences from domesticated rice accessions produce more branches and grains. Neither the molecular control of branching nor the developmental differences between wild and domesticated rice accessions are fully understood. We surveyed phenotypes related to branching, size, and grain yield across 91 wild and domesticated African and Asian accessions. Characteristics related to axillary meristem identity were the main phenotypic differences between inflorescences from wild and domesticated accessions. We used whole transcriptome sequencing in developing inflorescences to measure gene expression before and after the transition from branching axillary meristems to determinate spikelet meristems. We identified a core set of genes associated with axillary meristem identity in Asian and African rice, and another set associated with phenotypic variability between wild and domesticated accessions. AP2/EREBP-like genes were enriched in both sets, suggesting that they are key factors in inflorescence branching and rice domestication. Our work has identified new candidates in the molecular control of inflorescence development and grain yield, and provides a detailed description of the effects of domestication on phenotype and gene expression.
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Affiliation(s)
- Thomas W R Harrop
- Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, Dunedin, Aotearoa, New Zealand
| | | | - Ai My Luong
- University of Montpellier, DIADE, IRD, France
| | | | - Mathias Lorieux
- Rice genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia
| | | | - Hélène Adam
- University of Montpellier, DIADE, IRD, France
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48
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Advances in Molecular Genetics and Genomics of African Rice ( Oryza glaberrima Steud). PLANTS 2019; 8:plants8100376. [PMID: 31561516 PMCID: PMC6843444 DOI: 10.3390/plants8100376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 02/07/2023]
Abstract
African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. Challenges in deploying African rice genetic resources in rice improvement and the genomics efforts made in addressing them are highlighted.
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49
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Snodgrass SJ, Hufford MB. Domestication Genomics: Untangling the Complex History of African Rice. Curr Biol 2019; 28:R786-R788. [PMID: 30040938 DOI: 10.1016/j.cub.2018.05.072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Study of domestication is complex but essential to our understanding of evolutionary processes and for crop breeding. A new study analyzes genomic data from 163 lines of domesticated African rice and 83 lines of its wild relative, clarifying the history of African rice domestication.
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Affiliation(s)
- Samantha J Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
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50
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Scarcelli N, Cubry P, Akakpo R, Thuillet AC, Obidiegwu J, Baco MN, Otoo E, Sonké B, Dansi A, Djedatin G, Mariac C, Couderc M, Causse S, Alix K, Chaïr H, François O, Vigouroux Y. Yam genomics supports West Africa as a major cradle of crop domestication. SCIENCE ADVANCES 2019; 5:eaaw1947. [PMID: 31114806 PMCID: PMC6527260 DOI: 10.1126/sciadv.aaw1947] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/15/2019] [Indexed: 05/24/2023]
Abstract
While there has been progress in our understanding of the origin and history of agriculture in sub-Saharan Africa, a unified perspective is still lacking on where and how major crops were domesticated in the region. Here, we investigated the domestication of African yam (Dioscorea rotundata), a key crop in early African agriculture. Using whole-genome resequencing and statistical models, we show that cultivated yam was domesticated from a forest species. We infer that the expansion of African yam agriculture started in the Niger River basin. This result, alongside with the origins of African rice and pearl millet, supports the hypothesis that the vicinity of the Niger River was a major cradle of African agriculture.
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Affiliation(s)
| | | | | | | | - Jude Obidiegwu
- National Root Crops Research Institute, Umudike, PMB 7006, Umuahia, Abia State, Nigeria
| | | | - Emmanuel Otoo
- CSIR-Crops Research Institute, P.O. Box 3785, Fumesua-Kumasi, Ghana
| | - Bonaventure Sonké
- University of Yaoundé I, Laboratory of Plant Systematics and Ecology, P.O. Box 047, Yaoundé, Cameroon
| | - Alexandre Dansi
- National University of Sciences, Technologies, Engineering and Mathematics of Abomey, Laboratory BIORAVE, Dassa-Zoumè, Benin
| | - Gustave Djedatin
- National University of Sciences, Technologies, Engineering and Mathematics of Abomey, Laboratory BIORAVE, Dassa-Zoumè, Benin
| | | | | | - Sandrine Causse
- Cirad UMR AGAP, F-34398 Montpellier, France
- University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Karine Alix
- GQE–Le Moulon, INRA, Univ Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Hâna Chaïr
- Cirad UMR AGAP, F-34398 Montpellier, France
- University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Olivier François
- University Grenoble-Alpes, Grenoble INP, TIMC-IMAG CNRS UMR 5525, 38042 Grenoble Cedex, France
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