1
|
Rafat SA, Barbato M, Hajializadeh Valilou R, Moghaddam GH, Nematollahi A, Periasamy K, Pichler R, Ajmone Marsan P. Identification of genomic regions associated with resistance to gastrointestinal parasites in an indigenous sheep by single- and multiple-locus methods. Anim Genet 2024; 55:286-290. [PMID: 38200404 DOI: 10.1111/age.13392] [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: 05/01/2023] [Revised: 12/16/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024]
Abstract
We investigated the association between 157 SNPs located in 75 candidate genes involved in the immune system and proxy traits for resistance to gastrointestinal nematodes in sheep. A total of 211 lambs from eight flocks were sampled. Nematode eggs per gram were counted and classified as: (i) Strongyles, (ii) Nematodirus spp., (iii) Trichuris spp. and (iv) Marshallagia marshalli. Single- and multiple-locus models were used to test the marker-trait associations. Seven significant SNPs were identified on chromosomes OAR6, 15, 16, and 19. These findings provide insights for breeding nemarode-resistant traits in low-input production systems. General linear model, fixed and random model circulating probability unification, and Bayesian-information and linkage-disequilibrium iteratively nested keyway analyses identified a significant association between the eggs per gram of Strongyles nematodes and a specific variant of the PRLR gene.
Collapse
Affiliation(s)
- S A Rafat
- Department of Animal Science, Faculty of Agricultural Sciences, University of Tabriz, Tabriz, Iran
| | - M Barbato
- Department of Animal Science, Food and Nutrition - DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Dipartimento di Scienze Veterinarie, Università degli Studi di Messina, Messina, Italy
| | - R Hajializadeh Valilou
- Department of Animal Science, Faculty of Agricultural Sciences, University of Tabriz, Tabriz, Iran
| | - G H Moghaddam
- Department of Animal Science, Faculty of Agricultural Sciences, University of Tabriz, Tabriz, Iran
| | - A Nematollahi
- Faculty of Veterinary, University of Tabriz, Tabriz, Iran
| | - K Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, Vienna, Austria
| | - R Pichler
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, Vienna, Austria
| | - P Ajmone Marsan
- Department of Animal Science, Food and Nutrition - DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| |
Collapse
|
2
|
Kyu KL, Taylor CM, Douglas CA, Malik AI, Colmer TD, Siddique KHM, Erskine W. Genetic diversity and candidate genes for transient waterlogging tolerance in mungbean at the germination and seedling stages. FRONTIERS IN PLANT SCIENCE 2024; 15:1297096. [PMID: 38584945 PMCID: PMC10996369 DOI: 10.3389/fpls.2024.1297096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/26/2024] [Indexed: 04/09/2024]
Abstract
Mungbean [Vigna radiata var. radiata (L.) Wilczek] production in Asia is detrimentally affected by transient soil waterlogging caused by unseasonal and increasingly frequent extreme precipitation events. While mungbean exhibits sensitivity to waterlogging, there has been insufficient exploration of germplasm for waterlogging tolerance, as well as limited investigation into the genetic basis for tolerance to identify valuable loci. This research investigated the diversity of transient waterlogging tolerance in a mini-core germplasm collection of mungbean and identified candidate genes for adaptive traits of interest using genome-wide association studies (GWAS) at two critical stages of growth: germination and seedling stage (i.e., once the first trifoliate leaf had fully-expanded). In a temperature-controlled glasshouse, 292 genotypes were screened for tolerance after (i) 4 days of waterlogging followed by 7 days of recovery at the germination stage and (ii) 8 days of waterlogging followed by 7 days of recovery at the seedling stage. Tolerance was measured against drained controls. GWAS was conducted using 3,522 high-quality DArTseq-derived SNPs, revealing five significant associations with five phenotypic traits indicating improved tolerance. Waterlogging tolerance was positively correlated with the formation of adventitious roots and higher dry masses. FGGY carbohydrate kinase domain-containing protein was identified as a candidate gene for adventitious rooting and mRNA-uncharacterized LOC111241851, Caffeoyl-CoA O-methyltransferase At4g26220 and MORC family CW-type zinc finger protein 3 and zinc finger protein 2B genes for shoot, root, and total dry matter production. Moderate to high broad-sense heritability was exhibited for all phenotypic traits, including seed emergence (81%), adventitious rooting (56%), shoot dry mass (81%), root dry mass (79%) and SPAD chlorophyll content (70%). The heritability estimates, marker-trait associations, and identification of sources of waterlogging tolerant germplasm from this study demonstrate high potential for marker-assisted selection of tolerance traits to accelerate breeding of climate-resilient mungbean varieties.
Collapse
Affiliation(s)
- Khin Lay Kyu
- Centre for Plant Genetics and Breeding (PGB), UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | | | - Colin Andrew Douglas
- Department of Agriculture and Fisheries, Gatton Research Facility, Gatton, QLD, Australia
| | - Al Imran Malik
- Centre for Plant Genetics and Breeding (PGB), UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- International Center for Tropical Agriculture (CIAT-Asia), Lao PDR Office, Vientiane, Lao People’s Democratic Republic
| | - Timothy David Colmer
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - William Erskine
- Centre for Plant Genetics and Breeding (PGB), UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| |
Collapse
|
3
|
Liu B, Wang N, Yang R, Wang X, Luo P, Chen Y, Wang F, Li M, Weng J, Zhang D, Yong H, Han J, Zhou Z, Zhang X, Hao Z, Li X. ZmADF5, a Maize Actin-Depolymerizing Factor Conferring Enhanced Drought Tolerance in Maize. PLANTS (BASEL, SWITZERLAND) 2024; 13:619. [PMID: 38475468 DOI: 10.3390/plants13050619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 03/14/2024]
Abstract
Drought stress is seriously affecting the growth and production of crops, especially when agricultural irrigation still remains quantitatively restricted in some arid and semi-arid areas. The identification of drought-tolerant genes is important for improving the adaptability of maize under stress. Here, we found that a new member of the actin-depolymerizing factor (ADF) family; the ZmADF5 gene was tightly linked with a consensus drought-tolerant quantitative trait locus, and the significantly associated signals were detected through genome wide association analysis. ZmADF5 expression could be induced by osmotic stress and the application of exogenous abscisic acid. Its overexpression in Arabidopsis and maize helped plants to keep a higher survival rate after water-deficit stress, which reduced the stomatal aperture and the water-loss rate, as well as improved clearance of reactive oxygen species. Moreover, seventeen differentially expressed genes were identified as regulated by both drought stress and ZmADF5, four of which were involved in the ABA-dependent drought stress response. ZmADF5-overexpressing plants were also identified as sensitive to ABA during the seed germination and seedling stages. These results suggested that ZmADF5 played an important role in the response to drought stress.
Collapse
Affiliation(s)
- Bojuan Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Nan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding 071000, China
| | - Ruisi Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaonan Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ping Luo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fei Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mingshun Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianfeng Weng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Degui Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongjun Yong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jienan Han
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiqiang Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Texcoco 06600, Mexico
| | - Zhuanfang Hao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinhai Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
4
|
Haqani MI, Nakano M, Nagano AJ, Nakamura Y, Tsudzuki M. Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing. Sci Rep 2023; 13:21307. [PMID: 38042890 PMCID: PMC10693557 DOI: 10.1038/s41598-023-48293-0] [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: 01/06/2023] [Revised: 10/10/2023] [Accepted: 11/24/2023] [Indexed: 12/04/2023] Open
Abstract
This study was designed to perform an association analysis and identify SNP markers associated with production traits of Japanese quail using restriction-site-associated DNA sequencing. Weekly body weight data from 805 quail were collected from hatching to 16 weeks of age. A total number of 3990 eggs obtained from 399 female quail were used to assess egg quality traits. Egg-related traits were measured at the beginning of egg production (first stage) and at 12 weeks of age (second stage). Five eggs were analyzed at each stage. Traits, such as egg weight, egg length and short axes, eggshell strength and weight, egg equator thickness, yolk weight, diameter, and colour, albumen weight, age of first egg, total number of laid eggs, and egg production rate, were assessed. A total of 383 SNPs and 1151 associations as well as 734 SNPs and 1442 associations were identified in relation to quail production traits using general linear model (GLM) and mixed linear model (MLM) approaches, respectively. The GLM-identified SNPs were located on chromosomes 1-13, 15, 17-20, 24, 26-28, and Z, underlying phenotypic traits, except for egg and albumen weight at the first stage and yolk yellowness at the second stage. The MLM-identified SNPs were positioned on defined chromosomes associated with phenotypic traits except for the egg long axis at the second stage of egg production. Finally, 35 speculated genes were identified as candidate genes for the targeted traits based on their nearest positions. Our findings provide a deeper understanding and allow a more precise genetic improvement of production traits of Galliformes, particularly in Japanese quail.
Collapse
Affiliation(s)
- Mohammad Ibrahim Haqani
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan.
| | - Michiharu Nakano
- Faculty of Agriculture and Marine Sciences, Kochi University, Nankoku, Kochi, 783-8502, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, Yamagata, 997-0017, Japan
| | - Yoshiaki Nakamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan
| | - Masaoki Tsudzuki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan.
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan.
| |
Collapse
|
5
|
Lamkey CM, Lorenz AJ. A genomic analysis of the University of Nebraska Replicated Recurrent Selection program. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:243. [PMID: 37950832 DOI: 10.1007/s00122-023-04475-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/27/2023] [Indexed: 11/13/2023]
Abstract
The inbred-hybrid system of maize breeding closely resembles a reciprocal full-sib (RFS) selection program. Studying changes in genetic variation as a result of RFS selection can help illuminate long-standing questions regarding the relative roles of selection and genetic drift and help understand the nature of adaptation occurring in selection programs. The University of Nebraska-Lincoln Replicated Recurrent Selection (UNL-RpRS) program underwent eight cycles of replicated RFS and S1-progeny selection, making it a powerful system to study genomic changes accompanying selection for inter-population performance. The objectives of this study were to identify regions of the genome under selection after eight cycles of selection and evaluate the effect eight cycles of selection for inter-population full-sib performance had in expanding genome-wide and localized population structure. We address these questions with a large set of individuals sampled from the UNL-RpRS program with dense genotyping-by-sequence data. We found evidence of parallel selection signatures in the UNL-RpRS program, with a region on chromosome 7 being implicated in three of the four selection systems studied. Regions that displayed selection signatures across independently run selection programs represent regions likely to be capitalizing on standing genetic variation and support a soft sweep model of adaptation. We did not find selection to be a strong force in diverging populations undergoing RFS. This could be due to the nature of adaptation occurring in these populations, underlying gene action, or a result of unstable genetic topographies.
Collapse
Affiliation(s)
- Collin M Lamkey
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
- Corteva Agriscience, 19456 Hwy 22, Mankato, MN, 56001, USA
| | - Aaron J Lorenz
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
| |
Collapse
|
6
|
Divakar S, Jha RK, Kamat DN, Singh A. Validation of candidate gene-based EST-SSR markers for sugar yield in sugarcane. FRONTIERS IN PLANT SCIENCE 2023; 14:1273740. [PMID: 37965001 PMCID: PMC10641762 DOI: 10.3389/fpls.2023.1273740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023]
Abstract
Sugarcane (Saccharum spp.) is a widely cultivated crop that fulfils approximately 75% of the sucrose demand worldwide. Owing to its polyploidy and complex genetic nature, it is difficult to identify and map genes related to complex traits, such as sucrose content. However, association mapping is one of the alternatives for identifying genes or markers for marker-assisted selection. In the present study, EST-SSR primers were obtained from in silico studies. The functionality of each primer was tested using Blast2Go software, and 30 EST-SSR primers related to sugar content were selected. These markers were validated using association analysis. A total of 70 F1 diverse genotypes for sugar content were phenotypes with two check lines. All parameters related to sugar content were recorded. The results showed a significant variation between the genotypes for sugar yield traits such as Brix value, purity, and sucrose content, etc. Correlation studies revealed that the Brix%, sucrose content, and sucrose recovery were significantly correlated. An association analysis was performed using mixed linear model to avoid false positive associations. The association analysis revealed that the SEM 407 marker was significantly associated with Brix% and sucrose content. The SEM 407 primers are putatively related to diphosphate-fructose-6-phosphate 1-phosphotransferase which is associated with Brix% and sucrose content. This functional marker can be used for marker-assisted selection for sugar yield traits in sugarcane that could accelerate the sugarcane breeding program.
Collapse
Affiliation(s)
- S. Divakar
- Department of AB&MB, CBSH, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Samastipur, Bihar, India
| | - Ratnesh Kumar Jha
- Centre for Advanced Studies on Climate Change, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Samastipur, Bihar, India
| | - D. N. Kamat
- Sugarcane Research Institute, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Samastipur, Bihar, India
| | - Ashutosh Singh
- Centre for Advanced Studies on Climate Change, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Samastipur, Bihar, India
| |
Collapse
|
7
|
Szabo-Hever A, Singh G, Haugrud ARP, Running KLD, Seneviratne S, Zhang Z, Shi G, Bassi FM, Maccaferri M, Cattivelli L, Tuberosa R, Friesen TL, Liu Z, Xu SS, Faris JD. Association Mapping of Resistance to Tan Spot in the Global Durum Panel. PHYTOPATHOLOGY 2023; 113:1967-1978. [PMID: 37199466 DOI: 10.1094/phyto-02-23-0043-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr), is an important disease of durum and common wheat worldwide. Compared with common wheat, less is known about the genetics and molecular basis of tan spot resistance in durum wheat. We evaluated 510 durum lines from the Global Durum Wheat Panel (GDP) for sensitivity to the necrotrophic effectors (NEs) Ptr ToxA and Ptr ToxB and for reaction to Ptr isolates representing races 1 to 5. Overall, susceptible durum lines were most prevalent in South Asia, the Middle East, and North Africa. Genome-wide association analysis showed that the resistance locus Tsr7 was significantly associated with tan spot caused by races 2 and 3, but not races 1, 4, or 5. The NE sensitivity genes Tsc1 and Tsc2 were associated with susceptibility to Ptr ToxC- and Ptr ToxB-producing isolates, respectively, but Tsn1 was not associated with tan spot caused by Ptr ToxA-producing isolates, which further validates that the Tsn1-Ptr ToxA interaction does not play a significant role in tan spot development in durum. A unique locus on chromosome arm 2AS was associated with tan spot caused by race 4, a race once considered avirulent. A novel trait characterized by expanding chlorosis leading to increased disease severity caused by the Ptr ToxB-producing race 5 isolate DW5 was identified, and this trait was governed by a locus on chromosome 5B. We recommend that durum breeders select resistance alleles at the Tsr7, Tsc1, Tsc2, and the chromosome 2AS loci to obtain broad resistance to tan spot.
Collapse
Affiliation(s)
- Agnes Szabo-Hever
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | - Gurminder Singh
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102
| | - Amanda R Peters Haugrud
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | | | - Sudeshi Seneviratne
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102
| | - Zengcui Zhang
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | - Filippo M Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Institutes, Rabat 10101, Morocco
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40127, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Center for Genomics and Bioinformatics, Fiorenzuola d'Arda 29017, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40127, Italy
| | - Timothy L Friesen
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | - Steven S Xu
- U.S. Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA 94710
| | - Justin D Faris
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| |
Collapse
|
8
|
Liu Z, Sun H, Zhang Y, Du M, Xiang J, Li X, Chang Y, Sun J, Cheng X, Xiong M, Zhao Z, Liu E. Mining the candidate genes of rice panicle traits via a genome-wide association study. Front Genet 2023; 14:1239550. [PMID: 37732315 PMCID: PMC10507276 DOI: 10.3389/fgene.2023.1239550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/16/2023] [Indexed: 09/22/2023] Open
Abstract
Panicle traits are important for improving the panicle architecture and grain yield of rice. Therefore, we performed a genome-wide association study (GWAS) to analyze and determine the genetic determinants of five panicle traits. A total of 1.29 million single nucleotide polymorphism (SNP) loci were detected in 162 rice materials. We carried out a GWAS of panicle length (PL), total grain number per panicle (TGP), filled grain number per panicle (FGP), seed setting rate (SSR) and grain weight per panicle (GWP) in 2019, 2020 and 2021. Four quantitative trait loci (QTLs) for PL were detected on chromosomes 1, 6, and 9; one QTL for TGP, FGP, and GWP was detected on chromosome 4; two QTLs for FGP were detected on chromosomes 4 and 7; and one QTL for SSR was detected on chromosome 1. These QTLs were detected via a general linear model (GLM) and mixed linear model (MLM) in both years of the study period. In this study, the genomic best linear unbiased prediction (BLUP) method was used to verify the accuracy of the GWAS results. There are nine QTLs were both detected by the multi-environment GWAS method and the BLUP method. Moreover, further analysis revealed that three candidate genes, LOC_Os01g43700, LOC_Os09g25784, and LOC_Os04g47890, may be significantly related to panicle traits of rice. Haplotype analysis indicated that LOC_Os01g43700 and LOC_Os09g25784 are highly associated with PL and that LOC_Os04g47890 is highly associated with TGP, FGP, and GWP. Our results offer essential genetic information for the molecular improvement of panicle traits. The identified candidate genes and elite haplotypes could be used in marker-assisted selection to improve rice yield through pyramid breeding.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Erbao Liu
- College of Agronomy, Anhui Agricultural University, Hefei, China
| |
Collapse
|
9
|
Tan T, Atkinson EG. Strategies for the Genomic Analysis of Admixed Populations. Annu Rev Biomed Data Sci 2023; 6:105-127. [PMID: 37127050 PMCID: PMC10871708 DOI: 10.1146/annurev-biodatasci-020722-014310] [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] [Indexed: 05/03/2023]
Abstract
Admixed populations constitute a large portion of global human genetic diversity, yet they are often left out of genomics analyses. This exclusion is problematic, as it leads to disparities in the understanding of the genetic structure and history of diverse cohorts and the performance of genomic medicine across populations. Admixed populations have particular statistical challenges, as they inherit genomic segments from multiple source populations-the primary reason they have historically been excluded from genetic studies. In recent years, however, an increasing number of statistical methods and software tools have been developed to account for and leverage admixture in the context of genomics analyses. Here, we provide a survey of such computational strategies for the informed consideration of admixture to allow for the well-calibrated inclusion of mixed ancestry populations in large-scale genomics studies, and we detail persisting gaps in existing tools.
Collapse
Affiliation(s)
- Taotao Tan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA;
| | - Elizabeth G Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA;
| |
Collapse
|
10
|
Taranto F, Esposito S, De Vita P. Genomics for Yield and Yield Components in Durum Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2571. [PMID: 37447132 DOI: 10.3390/plants12132571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
In recent years, many efforts have been conducted to dissect the genetic basis of yield and yield components in durum wheat thanks to linkage mapping and genome-wide association studies. In this review, starting from the analysis of the genetic bases that regulate the expression of yield for developing new durum wheat varieties, we have highlighted how, currently, the reductionist approach, i.e., dissecting the yield into its individual components, does not seem capable of ensuring significant yield increases due to diminishing resources, land loss, and ongoing climate change. However, despite the identification of genes and/or chromosomal regions, controlling the grain yield in durum wheat is still a challenge, mainly due to the polyploidy level of this species. In the review, we underline that the next-generation sequencing (NGS) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms, as well as genome editing technology, will revolutionize plant breeding by providing a great opportunity to capture genetic variation that can be used in breeding programs. To date, genomic selection provides a valuable tool for modeling optimal allelic combinations across the whole genome that maximize the phenotypic potential of an individual under a given environment.
Collapse
Affiliation(s)
- Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), 70126 Bari, Italy
| | - Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, 71122 Foggia, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, 71122 Foggia, Italy
| |
Collapse
|
11
|
Peters Haugrud AR, Shi G, Seneviratne S, Running KLD, Zhang Z, Singh G, Szabo-Hever A, Acharya K, Friesen TL, Liu Z, Faris JD. Genome-wide association mapping of resistance to the foliar diseases septoria nodorum blotch and tan spot in a global winter wheat collection. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:54. [PMID: 37337566 PMCID: PMC10276793 DOI: 10.1007/s11032-023-01400-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Septoria nodorum blotch (SNB) and tan spot, caused by the necrotrophic fungal pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis, respectively, often occur together as a leaf spotting disease complex on wheat (Triticum aestivum L.). Both pathogens produce necrotrophic effectors (NEs) that contribute to the development of disease. Here, genome-wide association analysis of a diverse panel of 264 winter wheat lines revealed novel loci on chromosomes 5A and 5B associated with sensitivity to the NEs SnTox3 and SnTox5 in addition to the known sensitivity genes for NEs Ptr/SnToxA, SnTox1, SnTox3, and SnTox5. Sensitivity loci for SnTox267 and Ptr ToxB were not detected. Evaluation of the panel with five P. nodorum isolates for SNB development indicated the Snn3-SnTox3 and Tsn1-SnToxA interactions played significant roles in disease development along with additional QTL on chromosomes 2A and 2D, which may correspond to the Snn7-SnTox267 interaction. For tan spot, the Tsc1-Ptr ToxC interaction was associated with disease caused by two isolates, and a novel QTL on chromosome 7D was associated with a third isolate. The Tsn1-ToxA interaction was associated with SNB but not tan spot. Therefore some, but not all, of the previously characterized host gene-NE interactions in these pathosystems play significant roles in disease development in winter wheat. Based on these results, breeders should prioritize the selection of resistance alleles at the Tsc1, Tsn1, Snn3, and Snn7 loci as well as the 2A and 7D QTL to obtain good levels of resistance to SNB and tan spot in winter wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01400-5.
Collapse
Affiliation(s)
- Amanda R. Peters Haugrud
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102 USA
| | - Sudeshi Seneviratne
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102 USA
| | | | - Zengcui Zhang
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| | - Gurminder Singh
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102 USA
| | - Agnes Szabo-Hever
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| | - Krishna Acharya
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102 USA
| | - Timothy L. Friesen
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102 USA
| | - Justin D. Faris
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| |
Collapse
|
12
|
Pradhan AK, Budhlakoti N, Chandra Mishra D, Prasad P, Bhardwaj SC, Sareen S, Sivasamy M, Jayaprakash P, Geetha M, Nisha R, Shajitha P, Peter J, Kaur A, Kaur S, Vikas VK, Singh K, Kumar S. Identification of Novel QTLs/Defense Genes in Spring Wheat Germplasm Panel for Seedling and Adult Plant Resistance to Stem Rust and Their Validation Through KASP Marker Assays. PLANT DISEASE 2023:PDIS09222242RE. [PMID: 37311158 DOI: 10.1094/pdis-09-22-2242-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Stem rust is one of the major diseases threatening wheat production globally. To identify novel resistance quantitative trait loci (QTLs), we performed 35K Axiom Array SNP genotyping assays on an association mapping panel of 400 germplasm accessions, including Indian landraces, in conjunction with phenotyping for stem rust at seedling and adult plant stages. Association analyses using three genome wide association study (GWAS) models (CMLM, MLMM, and FarmCPU) revealed 20 reliable QTLs for seedling and adult plant resistance. Among these 20 QTLs, five QTLs were found consistent with three models, i.e., four QTLs on chromosome 2AL, 2BL, 2DL, and 3BL for seedling resistance and one QTL on chromosome 7DS for adult plant resistance. Further, we identified a total of 21 potential candidate genes underlying QTLs using gene ontology analysis, including a leucine rich repeat receptor (LRR) and P-loop nucleoside triphosphate hydrolase, which have a role in pathogen recognition and disease resistance. Furthermore, four QTLs (Qsr.nbpgr-3B_11, QSr.nbpgr-6AS_11, QSr.nbpgr-2AL_117-6, and QSr.nbpgr-7BS_APR) were validated through KASP located on chromosomes 3B, 6A, 2A, and 7B. Out of these QTLs, QSr.nbpgr-7BS_APR was identified as a novel QTL for stem rust resistance which has been found effective in both seedling as well as the adult plant stages. Identified novel genomic regions and validated QTLs have the potential to be deployed in wheat improvement programs to develop disease resistant varieties for stem rust and can diversify the genetic basis of resistance.
Collapse
Affiliation(s)
| | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | | | - Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh 171002, India
| | - S C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh 171002, India
| | - Sindhu Sareen
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - M Sivasamy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - P Jayaprakash
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - M Geetha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - R Nisha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - P Shajitha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - John Peter
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - Amandeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India
| | - V K Vikas
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - Kuldeep Singh
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana 502324, India
| | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| |
Collapse
|
13
|
Vallarino JG, Jun H, Wang S, Wang X, Sade N, Orf I, Zhang D, Shi J, Shen S, Cuadros-Inostroza Á, Xu Q, Luo J, Fernie AR, Brotman Y. Limitations and advantages of using metabolite-based genome-wide association studies: focus on fruit quality traits. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 333:111748. [PMID: 37230189 DOI: 10.1016/j.plantsci.2023.111748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 05/27/2023]
Abstract
In the last decades, linkage mapping has help in the location of metabolite quantitative trait loci (QTL) in many species; however, this approach shows some limitations. Recently, thanks to the most recent advanced in high-throughput genotyping technologies like next-generation sequencing, metabolite genome-wide association study (mGWAS) has been proposed a powerful tool to identify the genetic variants in polygenic agrinomic traits. Fruit flavor is a complex interaction of aroma volatiles and taste being sugar and acid ratio key parameter for flavor acceptance. Here, we review recent progress of mGWAS in pinpoint gene polymorphisms related to flavor-related metabolites in fruits. Despite clear successes in discovering novel genes or regions associated with metabolite accumulation affecting sensory attributes in fruits, GWAS incurs in several limitations summarized in this review. In addition, in our own work, we performed mGWAS on 194 Citrus grandis accessions to investigate the genetic control of individual primary and lipid metabolites in ripe fruit. We have identified a total of 667 associations for 14 primary metabolites including amino acids, sugars, and organic acids, and 768 associations corresponding to 47 lipids. Furthermore, candidate genes related to important metabolites related to fruit quality such as sugars, organic acids and lipids were discovered.
Collapse
Affiliation(s)
- José G Vallarino
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Campus de Teatinos, 29071 Málaga, Spain
| | - Hong Jun
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | | | - Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Isabel Orf
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Dabing Zhang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Jianxin Shi
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | | | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Alisdair R Fernie
- Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Mühlenberg, Golm, Potsdam 14476, Germany; Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria.
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel.
| |
Collapse
|
14
|
Knutson KA, Pan W. MATS: a novel multi-ancestry transcriptome-wide association study to account for heterogeneity in the effects of cis-regulated gene expression on complex traits. Hum Mol Genet 2023; 32:1237-1251. [PMID: 36179104 PMCID: PMC10077507 DOI: 10.1093/hmg/ddac247] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/16/2022] [Accepted: 09/28/2022] [Indexed: 01/16/2023] Open
Abstract
The Transcriptome-Wide Association Study (TWAS) is a widely used approach which integrates gene expression and Genome Wide Association Study (GWAS) data to study the role of cis-regulated gene expression (GEx) in complex traits. However, the genetic architecture of GEx varies across populations, and recent findings point to possible ancestral heterogeneity in the effects of GEx on complex traits, which may be amplified in TWAS by modeling GEx as a function of cis-eQTLs. Here, we present a novel extension to TWAS to account for heterogeneity in the effects of cis-regulated GEx which are correlated with ancestry. Our proposed Multi-Ancestry TwaS (MATS) framework jointly analyzes samples from multiple populations and distinguishes between shared, ancestry-specific and/or subject-specific expression-trait associations. As such, MATS amplifies power to detect shared GEx associations over ancestry-stratified TWAS through increased sample sizes, and facilitates the detection of genes with subgroup-specific associations which may be masked by standard TWAS. Our simulations highlight the improved Type-I error conservation and power of MATS compared with competing approaches. Our real data applications to Alzheimer's disease (AD) case-control genotypes from the Alzheimer's Disease Sequencing Project (ADSP) and continuous phenotypes from the UK Biobank (UKBB) identify a number of unique gene-trait associations which were not discovered through standard and/or ancestry-stratified TWAS. Ultimately, these findings promote MATS as a powerful method for detecting and estimating significant gene expression effects on complex traits within multi-ancestry cohorts and corroborates the mounting evidence for inter-population heterogeneity in gene-trait associations.
Collapse
Affiliation(s)
| | - Wei Pan
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
15
|
Coolen S, Van Dijen M, Van Pelt JA, Van Loon JJA, Pieterse CMJ, Van Wees SCM. Genome-wide association study reveals WRKY42 as a novel plant transcription factor that influences oviposition preference of Pieris butterflies. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:1690-1704. [PMID: 36560910 PMCID: PMC10010613 DOI: 10.1093/jxb/erac501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Insect herbivores are amongst the most destructive plant pests, damaging both naturally occurring and domesticated plants. As sessile organisms, plants make use of structural and chemical barriers to counteract herbivores. However, over 75% of herbivorous insect species are well adapted to their host's defenses and these specialists are generally difficult to ward off. By actively antagonizing the number of insect eggs deposited on plants, future damage by the herbivore's offspring can be limited. Therefore, it is important to understand which plant traits influence attractiveness for oviposition, especially for specialist insects that are well adapted to their host plants. In this study, we investigated the oviposition preference of Pieris butterflies (Lepidoptera: Pieridae) by offering them the choice between 350 different naturally occurring Arabidopsis accessions. Using a genome-wide association study of the oviposition data and subsequent fine mapping with full genome sequences of 164 accessions, we identified WRKY42 and AOC1 as candidate genes that are associated with the oviposition preference observed for Pieris butterflies. Host plant choice assays with Arabidopsis genotypes impaired in WRKY42 or AOC1 function confirmed a clear role for WRKY42 in oviposition preference of female Pieris butterflies, while for AOC1 the effect was mild. In contrast, WRKY42-impaired plants, which were preferred for oviposition by butterflies, negatively impacted offspring performance. These findings exemplify that plant genotype can have opposite effects on oviposition preference and caterpillar performance. This knowledge can be used for breeding trap crops or crops that are unattractive for oviposition by pest insects.
Collapse
Affiliation(s)
| | - Marcel Van Dijen
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Johan A Van Pelt
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Joop J A Van Loon
- Laboratory of Entomology, Wageningen University, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Saskia C M Van Wees
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| |
Collapse
|
16
|
Sa KJ, Park H, Jang SJ, Lee JK. Association Mapping of Amylose Content in Maize RIL Population Using SSR and SNP Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:239. [PMID: 36678952 PMCID: PMC9865990 DOI: 10.3390/plants12020239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
The ratio of amylose to amylopectin in maize kernel starch is important for the appearance, structure, and quality of food products and processing. This study aimed to identify quantitative trait loci (QTLs) controlling amylose content in maize through association mapping with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. The average value of amylose content for an 80-recombinant-inbred-line (RIL) population was 8.8 ± 0.7%, ranging from 2.1 to 15.9%. We used two different analyses-Q + K and PCA + K mixed linear models (MLMs)-and found 38 (35 SNP and 3 SSR) and 32 (29 SNP and 3 SSR) marker-trait associations (MTAs) associated with amylose content. A total of 34 (31 SNP and 3 SSR) and 28 (25 SNP and 3 SSR) MTAs were confirmed in the Q + K and PCA + K MLMs, respectively. This study detected some candidate genes for amylose content, such as GRMZM2G118690-encoding BBR/BPC transcription factor, which is used for the control of seed development and is associated with the amylose content of rice. GRMZM5G830776-encoding SNARE-interacting protein (KEULE) and the uncharacterized marker PUT-163a-18172151-1376 were significant with higher R2 value in two difference methods. GRMZM2G092296 were also significantly associated with amylose content in this study. This study focused on amylose content using a RIL population derived from dent and waxy inbred lines using molecular markers. Future studies would be of benefit for investigating the physical linkage between starch synthesis genes using SNP and SSR markers, which would help to build a more detailed genetic map and provide new insights into gene regulation of agriculturally important traits.
Collapse
Affiliation(s)
- Kyu Jin Sa
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hyeon Park
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - So Jung Jang
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Ju Kyong Lee
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Republic of Korea
| |
Collapse
|
17
|
Zhang H, Tang Y, Li Q, Zhao S, Zhang Z, Chen Y, Shen Z, Chen C. Genetic and epigenetic variation separately contribute to range expansion and local metalliferous habitat adaptation during invasions of Chenopodium ambrosioides into China. ANNALS OF BOTANY 2022; 130:1041-1056. [PMID: 36413156 PMCID: PMC9851312 DOI: 10.1093/aob/mcac139] [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: 09/21/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS Invasive plants often colonize wide-ranging geographical areas with various local microenvironments. The specific roles of epigenetic and genetic variation during such expansion are still unclear. Chenopodium ambrosioides is a well-known invasive alien species in China that can thrive in metalliferous habitats. This study aims to comprehensively understand the effects of genetic and epigenetic variation on the successful invasion of C. ambrosioides. METHODS We sampled 367 individuals from 21 heavy metal-contaminated and uncontaminated sites with a wide geographical distribution in regions of China. We obtained environmental factors of these sampling sites, including 13 meteorological factors and the contents of four heavy metals in soils. Microsatellite markers were used to investigate the demographic history of C. ambrosioides populations in China. We also analysed the effect of epigenetic variation on metalliferous microhabitat adaptation using methylation-sensitive amplified polymorphism (MSAP) markers. A common garden experiment was conducted to compare heritable phenotypic variations among populations. KEY RESULTS Two distinct genetic clusters that diverged thousands of years ago were identified, suggesting that the eastern and south-western C. ambrosioides populations in China may have originated from independent introduction events without recombination. Genetic variation was shown to be a dominant determinant of phenotypic differentiation relative to epigenetic variation, and further affected the geographical distribution pattern of invasive C. ambrosioides. The global DNA unmethylation level was reduced in metalliferous habitats. Dozens of methylated loci were significantly associated with the heavy metal accumulation trait of C. ambrosioides and may contribute to coping with metalliferous microenvironments. CONCLUSIONS Our study of C. ambrosioides highlighted the dominant roles of genetic variation in large geographical range expansion and epigenetic variation in local metalliferous habitat adaptation.
Collapse
Affiliation(s)
- Hanchao Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Yongwei Tang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Quanyuan Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Shangjun Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Zhou Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| |
Collapse
|
18
|
Wilkinson MJ, Yamashita R, James ME, Bally ISE, Dillon NL, Ali A, Hardner CM, Ortiz-Barrientos D. The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool. Sci Rep 2022; 12:20614. [PMID: 36450793 PMCID: PMC9712640 DOI: 10.1038/s41598-022-24800-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/21/2022] [Indexed: 12/11/2022] Open
Abstract
Genomic selection is a promising breeding technique for tree crops to accelerate the development of new cultivars. However, factors such as genetic structure can create spurious associations between genotype and phenotype due to the shared history between populations with different trait values. Genetic structure can therefore reduce the accuracy of the genotype to phenotype map, a fundamental requirement of genomic selection models. Here, we employed 272 single nucleotide polymorphisms from 208 Mangifera indica accessions to explore whether the genetic structure of the Australian mango gene pool explained variation in trunk circumference, fruit blush colour and intensity. Multiple population genetic analyses indicate the presence of four genetic clusters and show that the most genetically differentiated cluster contains accessions imported from Southeast Asia (mainly those from Thailand). We find that genetic structure was strongly associated with three traits: trunk circumference, fruit blush colour and intensity in M. indica. This suggests that the history of these accessions could drive spurious associations between loci and key mango phenotypes in the Australian mango gene pool. Incorporating such genetic structure in associations between genotype and phenotype can improve the accuracy of genomic selection, which can assist the future development of new cultivars.
Collapse
Affiliation(s)
- Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Risa Yamashita
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Maddie E James
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ian S E Bally
- Queensland Department of Agriculture and Fisheries, Mareeba, QLD, 4880, Australia
| | - Natalie L Dillon
- Queensland Department of Agriculture and Fisheries, Mareeba, QLD, 4880, Australia
| | - Asjad Ali
- Queensland Department of Agriculture and Fisheries, Mareeba, QLD, 4880, Australia
| | - Craig M Hardner
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, 4072, Australia
| |
Collapse
|
19
|
Genome-wide association studies and genomic selection assays made in a large sample of cacao (Theobroma cacao L.) germplasm reveal significant marker-trait associations and good predictive value for improving yield potential. PLoS One 2022; 17:e0260907. [PMID: 36201531 PMCID: PMC9536643 DOI: 10.1371/journal.pone.0260907] [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: 11/17/2021] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
A genome-wide association study (GWAS) was undertaken to unravel marker-trait associations (MTAs) between SNP markers and phenotypic traits. It involved a subset of 421 cacao accessions from the large and diverse collection conserved ex situ at the International Cocoa Genebank Trinidad. A Mixed Linear Model (MLM) in TASSEL was used for the GWAS and followed by confirmatory analyses using GAPIT FarmCPU. An average linkage disequilibrium (r2) of 0.10 at 5.2 Mb was found across several chromosomes. Seventeen significant (P ≤ 8.17 × 10-5 (-log10 (p) = 4.088)) MTAs of interest, including six that pertained to yield-related traits, were identified using TASSEL MLM. The latter accounted for 5 to 17% of the phenotypic variation expressed. The highly significant association (P ≤ 8.17 × 10-5) between seed length to width ratio and TcSNP 733 on chromosome 5 was verified with FarmCPU (P ≤ 1.12 × 10-8). Fourteen MTAs were common to both the TASSEL and FarmCPU models at P ≤ 0.003. The most significant yield-related MTAs involved seed number and seed length on chromosome 7 (P ≤ 1.15 × 10-14 and P ≤ 6.75 × 10-05, respectively) and seed number on chromosome 1 (P ≤ 2.38 × 10-05), based on the TASSEL MLM. It was noteworthy that seed length, seed length to width ratio and seed number were associated with markers at different loci, indicating their polygenic nature. Approximately 40 candidate genes that encode embryo and seed development, protein synthesis, carbohydrate transport and lipid biosynthesis and transport were identified in the flanking regions of the significantly associated SNPs and in linkage disequilibrium with them. A significant association of fruit surface anthocyanin intensity co-localised with MYB-related protein 308 on chromosome 4. Testing of a genomic selection approach revealed good predictive value (genomic estimated breeding values (GEBV)) for economic traits such as seed number (GEBV = 0.611), seed length (0.6199), seed width (0.5435), seed length to width ratio (0.5503), seed/cotyledon mass (0.6014) and ovule number (0.6325). The findings of this study could facilitate genomic selection and marker-assisted breeding of cacao thereby expediting improvement in the yield potential of cacao planting material.
Collapse
|
20
|
Widmayer SJ, Evans KS, Zdraljevic S, Andersen EC. Evaluating the power and limitations of genome-wide association studies in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2022; 12:6583190. [PMID: 35536194 PMCID: PMC9258552 DOI: 10.1093/g3journal/jkac114] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/02/2022] [Indexed: 11/30/2022]
Abstract
Quantitative genetics in Caenorhabditis elegans seeks to identify naturally segregating genetic variants that underlie complex traits. Genome-wide association studies scan the genome for individual genetic variants that are significantly correlated with phenotypic variation in a population, or quantitative trait loci. Genome-wide association studies are a popular choice for quantitative genetic analyses because the quantitative trait loci that are discovered segregate in natural populations. Despite numerous successful mapping experiments, the empirical performance of genome-wide association study has not, to date, been formally evaluated in C. elegans. We developed an open-source genome-wide association study pipeline called NemaScan and used a simulation-based approach to provide benchmarks of mapping performance in collections of wild C. elegans strains. Simulated trait heritability and complexity determined the spectrum of quantitative trait loci detected by genome-wide association studies. Power to detect smaller-effect quantitative trait loci increased with the number of strains sampled from the C. elegans Natural Diversity Resource. Population structure was a major driver of variation in mapping performance, with populations shaped by recent selection exhibiting significantly lower false discovery rates than populations composed of more divergent strains. We also recapitulated previous genome-wide association studies of experimentally validated quantitative trait variants. Our simulation-based evaluation of performance provides the community with critical context to pursue quantitative genetic studies using the C. elegans Natural Diversity Resource to elucidate the genetic basis of complex traits in C. elegans natural populations.
Collapse
Affiliation(s)
- Samuel J Widmayer
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Kathryn S Evans
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Stefan Zdraljevic
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| |
Collapse
|
21
|
Cao S, Duan H, Sun Y, Hu R, Wu B, Lin J, Deng W, Li Y, Zheng H. Genome-Wide Association Study With Growth-Related Traits and Secondary Metabolite Contents in Red- and White-Heart Chinese Fir. FRONTIERS IN PLANT SCIENCE 2022; 13:922007. [PMID: 35845628 PMCID: PMC9280351 DOI: 10.3389/fpls.2022.922007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Chinese fir [Cunninghamia lanceolata (Lamb.) Hook] is an important evergreen coniferous tree species that is widely distributed in many southern provinces of China and has important economic value. The Chinese fir accounts for 1/4 and 1/3 of the total artificial forest area and stock volume, respectively. Red-heart Chinese fir is popular in the market because of its high density and red heartwood. The long-growth cycle hindered the breeding process of Chinese fir, while molecular marker-assisted breeding could accelerate it. However, Chinese fir, a perennial conifer species, has a large genome, which has not yet been published. In this study, the growth-related traits and secondary metabolite contents of red- and white-heart Chinese fir were measured and found to be different between them. There are extremely significant differences among growth-related traits (p < 0.001), but secondary metabolite contents have different correlations due to differences in chemical structure. Moreover, genotype effect analysis of the substantially correlated single nucleotide polymorphisms (SNPs) revealed that most of the loci related to each growth-related traits were different from each other, indicating a type specificity of the genes regulated different growth-related traits. Furthermore, among the loci related to secondary metabolite contents, nine loci associated with multiple metabolite phenotypes such as Marker21022_4, Marker21022_172, Marker24559_31, Marker27425_37, Marker20748_85, Marker18841_115, Marker18841_198, Marker65846_146, and Marker21486_163, suggesting the presence of pleiotropic genes. This study identified the potential SNP markers associated with secondary metabolites in Chinese fir, thus setting the basis for molecular marker-assisted selection.
Collapse
Affiliation(s)
- Sen Cao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongjing Duan
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Experimental School Affiliated to Chinese Academy of Sciences, Beijing, China
| | - Yuhan Sun
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ruiyang Hu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, China
| | - Bo Wu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jun Lin
- Longshan State Forest Farm of Lechang, Lechang, China
| | - Wenjian Deng
- Longshan State Forest Farm of Lechang, Lechang, China
| | - Yun Li
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Huiquan Zheng
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| |
Collapse
|
22
|
Fang Z, Peltz G. An automated multi-modal graph-based pipeline for mouse genetic discovery. Bioinformatics 2022; 38:3385-3394. [PMID: 35608290 PMCID: PMC9992076 DOI: 10.1093/bioinformatics/btac356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/18/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Our ability to identify causative genetic factors for mouse genetic models of human diseases and biomedical traits has been limited by the difficulties associated with identifying true causative factors, which are often obscured by the many false positive genetic associations produced by a GWAS. RESULTS To accelerate the pace of genetic discovery, we developed a graph neural network (GNN)-based automated pipeline (GNNHap) that could rapidly analyze mouse genetic model data and identify high probability causal genetic factors for analyzed traits. After assessing the strength of allelic associations with the strain response pattern; this pipeline analyzes 29M published papers to assess candidate gene-phenotype relationships; and incorporates the information obtained from a protein-protein interaction network and protein sequence features into the analysis. The GNN model produces markedly improved results relative to that of a simple linear neural network. We demonstrate that GNNHap can identify novel causative genetic factors for murine models of diabetes/obesity and for cataract formation, which were validated by the phenotypes appearing in previously analyzed gene knockout mice. The diabetes/obesity results indicate how characterization of the underlying genetic architecture enables new therapies to be discovered and tested by applying 'precision medicine' principles to murine models. AVAILABILITY AND IMPLEMENTATION The GNNHap source code is freely available at https://github.com/zqfang/gnnhap, and the new version of the HBCGM program is available at https://github.com/zqfang/haplomap. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Zhuoqing Fang
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gary Peltz
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
23
|
Jing M, Zhang H, Wei M, Tang Y, Xia Y, Chen Y, Shen Z, Chen C. Reactive Oxygen Species Partly Mediate DNA Methylation in Responses to Different Heavy Metals in Pokeweed. FRONTIERS IN PLANT SCIENCE 2022; 13:845108. [PMID: 35463456 PMCID: PMC9021841 DOI: 10.3389/fpls.2022.845108] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
DNA methylation is a rapid response strategy promoting plant survival under heavy metal (HM) stress. However, the roles of DNA methylation underlying plant adaptation to HM stress remain largely unknown. Here, we used pokeweed, a hyperaccumulator of manganese (Mn) and cadmium (Cd), to explore responses of plant to HM stress at phenotypic, transcriptional and DNA methylation levels. Mn- and Cd-specific response patterns were detected in pokeweed. The growth of pokeweed was both inhibited with exposure to excess Mn/Cd, but pokeweed distinguished Mn and Cd with different subcellular distributions, ROS scavenging systems, transcriptional patterns including genes involved in DNA methylation, and differentially methylated loci (DML). The number of DML between Mn/Cd treated and untreated samples increased with increased Mn/Cd concentrations. Meanwhile, pretreatment with NADPH oxidase inhibitors prior to HM exposure markedly reduced HM-induced reactive oxygen species (ROS), which caused reductions in expressions of DNA methylase and demethylase in pretreated samples. The increased levels of HM-induced demethylation were suppressed with alleviated ROS stress, and a series of HM-related methylated loci were also ROS-related. Taken together, our study demonstrates that different HMs affect different DNA methylation sites in a dose-dependent manner and changes in DNA methylation under Mn/Cd stress are partly mediated by HM-induced ROS.
Collapse
Affiliation(s)
- Minyu Jing
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hanchao Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mingyue Wei
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yongwei Tang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yan Xia
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
24
|
Giordani W, Gama HC, Chiorato AF, Garcia AAF, Vieira MLC. Genome-wide association studies dissect the genetic architecture of seed shape and size in common bean. G3 (BETHESDA, MD.) 2022; 12:jkac048. [PMID: 35218340 PMCID: PMC8982408 DOI: 10.1093/g3journal/jkac048] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Seed weight and size are important yield components. Thus, selecting for large seeds has been a key objective in crop domestication and breeding. In common bean, seed shape is also important since it influences industrial processing and plays a vital role in determining the choices of consumers and farmers. In this study, we performed genome-wide association studies on a core collection of common bean accessions to dissect the genetic architecture and identify genomic regions associated with seed morphological traits related to weight, size, and shape. Phenotypic data were collected by high-throughput image-based approaches, and utilized to test associations with 10,362 single-nucleotide polymorphism markers using multilocus mixed models. We searched within genome-associated regions for candidate genes putatively involved in seed phenotypic variation. The collection exhibited high variability for the entire set of seed traits, and the Andean gene pool was found to produce larger, heavier seeds than the Mesoamerican gene pool. Strong pairwise correlations were verified for most seed traits. Genome-wide association studies identified marker-trait associations accounting for a considerable amount of phenotypic variation in length, width, projected area, perimeter, and circularity in 4 distinct genomic regions. Promising candidate genes were identified, e.g. those encoding an AT-hook motif nuclear-localized protein 8, type 2C protein phosphatases, and a protein Mei2-like 4 isoform, known to be associated with seed size and weight regulation. Moreover, the genes that were pinpointed are also good candidates for functional analysis to validate their influence on seed shape and size in common bean and other related crops.
Collapse
Affiliation(s)
- Willian Giordani
- Department of Genetics, ‘Luiz de Queiroz’ College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Henrique Castro Gama
- Department of Genetics, ‘Luiz de Queiroz’ College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | | | - Antonio Augusto Franco Garcia
- Department of Genetics, ‘Luiz de Queiroz’ College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Maria Lucia Carneiro Vieira
- Department of Genetics, ‘Luiz de Queiroz’ College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| |
Collapse
|
25
|
Matsui T, Mullis MN, Roy KR, Hale JJ, Schell R, Levy SF, Ehrenreich IM. The interplay of additivity, dominance, and epistasis on fitness in a diploid yeast cross. Nat Commun 2022; 13:1463. [PMID: 35304450 PMCID: PMC8933436 DOI: 10.1038/s41467-022-29111-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/22/2022] [Indexed: 12/27/2022] Open
Abstract
In diploid species, genetic loci can show additive, dominance, and epistatic effects. To characterize the contributions of these different types of genetic effects to heritable traits, we use a double barcoding system to generate and phenotype a panel of ~200,000 diploid yeast strains that can be partitioned into hundreds of interrelated families. This experiment enables the detection of thousands of epistatic loci, many whose effects vary across families. Here, we show traits are largely specified by a small number of hub loci with major additive and dominance effects, and pervasive epistasis. Genetic background commonly influences both the additive and dominance effects of loci, with multiple modifiers typically involved. The most prominent dominance modifier in our data is the mating locus, which has no effect on its own. Our findings show that the interplay between additivity, dominance, and epistasis underlies a complex genotype-to-phenotype map in diploids.
Collapse
Affiliation(s)
- Takeshi Matsui
- Joint Initiative for Metrology in Biology, Stanford, CA, 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Martin N Mullis
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
- Twist Bioscience, 681 Gateway Blvd, South San Francisco, CA, 94080, USA
| | - Kevin R Roy
- Joint Initiative for Metrology in Biology, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA
| | - Joseph J Hale
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Rachel Schell
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Sasha F Levy
- Joint Initiative for Metrology in Biology, Stanford, CA, 94305, USA.
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| |
Collapse
|
26
|
Giordani W, Gama HC, Chiorato AF, Marques JPR, Huo H, Benchimol-Reis LL, Camargo LEA, Garcia AAF, Vieira MLC. Genetic mapping reveals complex architecture and candidate genes involved in common bean response to Meloidogyne incognita infection. THE PLANT GENOME 2022; 15:e20161. [PMID: 34806826 DOI: 10.1002/tpg2.20161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Root-knot nematodes (RKNs), particularly Meloidogyne incognita, are among the most damaging and prevalent agricultural pathogens due to their ability to infect roots of almost all crops. The best strategy for their control is through the use of resistant cultivars. However, laborious phenotyping procedures make it difficult to assess nematode resistance in breeding programs. For common bean, this task is especially challenging because little has been done to discover resistance genes or markers to assist selection. We performed genome-wide association studies and quantitative trait loci mapping to explore the genetic architecture and genomic regions underlying the resistance to M. incognita and to identify candidate resistance genes. Phenotypic data were collected by a high-throughput assay, and the number of egg masses and the root-galling index were evaluated. Complex genetic architecture and independent genomic regions were associated with each trait. Single nucleotide polymorphisms on chromosomes Pv06, Pv07, Pv08, and Pv11 were associated with the number of egg masses, and SNPs on Pv01, Pv02, Pv05, and Pv10 were associated with root-galling. A total of 216 candidate genes were identified, including 14 resistance gene analogs and five differentially expressed in a previous RNA sequencing analysis. Histochemical analysis indicated that reactive oxygen species might play a role in the resistance response. Our findings open new perspectives to improve selection efficiency for RKN resistance, and the candidate genes are valuable targets for functional investigation and gene editing approaches.
Collapse
Affiliation(s)
- Willian Giordani
- "Luiz de Queiroz" College of Agriculture, Univ. of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | - Henrique Castro Gama
- "Luiz de Queiroz" College of Agriculture, Univ. of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | | | | | - Heqiang Huo
- Mid-Florida Research and Education Center, Univ. of Florida, Apopka, FL, 32703, USA
| | | | | | | | | |
Collapse
|
27
|
Gawarecka K, Siwinska J, Poznanski J, Onysk A, Surowiecki P, Sztompka K, Surmacz L, Ahn JH, Korte A, Swiezewska E, Ihnatowicz A. cis-prenyltransferase 3 and α/β-hydrolase are new determinants of dolichol accumulation in Arabidopsis. PLANT, CELL & ENVIRONMENT 2022; 45:479-495. [PMID: 34778961 PMCID: PMC9300173 DOI: 10.1111/pce.14223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 11/06/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Dolichols (Dols), ubiquitous components of living organisms, are indispensable for cell survival. In plants, as well as other eukaryotes, Dols are crucial for post-translational protein glycosylation, aberration of which leads to fatal metabolic disorders in humans and male sterility in plants. Until now, the mechanisms underlying Dol accumulation remain elusive. In this study, we have analysed the natural variation of the accumulation of Dols and six other isoprenoids among more than 120 Arabidopsis thaliana accessions. Subsequently, by combining QTL and GWAS approaches, we have identified several candidate genes involved in the accumulation of Dols, polyprenols, plastoquinone and phytosterols. The role of two genes implicated in the accumulation of major Dols in Arabidopsis-the AT2G17570 gene encoding a long searched for cis-prenyltransferase (CPT3) and the AT1G52460 gene encoding an α/β-hydrolase-is experimentally confirmed. These data will help to generate Dol-enriched plants which might serve as a remedy for Dol-deficiency in humans.
Collapse
Affiliation(s)
- Katarzyna Gawarecka
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarszawaPoland
- Department of Life SciencesKorea UniversitySeoulKorea
| | - Joanna Siwinska
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of GdanskUniversity of GdanskGdanskPoland
| | - Jaroslaw Poznanski
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarszawaPoland
| | - Agnieszka Onysk
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarszawaPoland
| | | | - Karolina Sztompka
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarszawaPoland
| | - Liliana Surmacz
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarszawaPoland
| | - Ji Hoon Ahn
- Department of Life SciencesKorea UniversitySeoulKorea
| | - Arthur Korte
- Center for Computational and Theoretical BiologyUniversity of WurzburgWurzburgGermany
| | - Ewa Swiezewska
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarszawaPoland
| | - Anna Ihnatowicz
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of GdanskUniversity of GdanskGdanskPoland
| |
Collapse
|
28
|
Peltz G, Tan Y. What Have We Learned (or Expect to) From Analysis of Murine Genetic Models Related to Substance Use Disorders? Front Psychiatry 2022; 12:793961. [PMID: 35095607 PMCID: PMC8790171 DOI: 10.3389/fpsyt.2021.793961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022] Open
Abstract
The tremendous public health problem created by substance use disorders (SUDs) presents a major opportunity for mouse genetics. Inbred mouse strains exhibit substantial and heritable differences in their responses to drugs of abuse (DOA) and in many of the behaviors associated with susceptibility to SUD. Therefore, genetic discoveries emerging from analysis of murine genetic models can provide critically needed insight into the neurobiological effects of DOA, and they can reveal how genetic factors affect susceptibility drug addiction. There are already indications, emerging from our prior analyses of murine genetic models of responses related to SUDs that mouse genetic models of SUD can provide actionable information, which can lead to new approaches for alleviating SUDs. Lastly, we consider the features of murine genetic models that enable causative genetic factors to be successfully identified; and the methodologies that facilitate genetic discovery.
Collapse
Affiliation(s)
- Gary Peltz
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | | |
Collapse
|
29
|
Yoosefzadeh-Najafabadi M, Eskandari M, Belzile F, Torkamaneh D. Genome-Wide Association Study Statistical Models: A Review. Methods Mol Biol 2022; 2481:43-62. [PMID: 35641758 DOI: 10.1007/978-1-0716-2237-7_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Statistical models are at the core of the genome-wide association study (GWAS). In this chapter, we provide an overview of single- and multilocus statistical models, Bayesian, and machine learning approaches for association studies in plants. These models are discussed based on their basic methodology, cofactors adjustment accounted for, statistical power and computational efficiency. New statistical models and machine learning algorithms are both showing improved performance in detecting missed signals, rare mutations and prioritizing causal genetic variants; nevertheless, further optimization and validation studies are required to maximize the power of GWAS.
Collapse
Affiliation(s)
| | - Milad Eskandari
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Quebec City, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.
| |
Collapse
|
30
|
Exploring the legacy of Central European historical winter wheat landraces. Sci Rep 2021; 11:23915. [PMID: 34903761 PMCID: PMC8668957 DOI: 10.1038/s41598-021-03261-4] [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: 06/18/2021] [Accepted: 11/29/2021] [Indexed: 11/14/2022] Open
Abstract
Historical wheat landraces are rich sources of genetic diversity offering untapped reservoirs for broadening the genetic base of modern varieties. Using a 20K SNP array, we investigated the accessible genetic diversity in a Central European bread wheat landrace collection with great drought, heat stress tolerance and higher tillering capacity. We discovered distinct differences in the number of average polymorphisms between landraces and modern wheat cultivars, and identified a set of novel rare alleles present at low frequencies in the landrace collection. The detected polymorphisms were unevenly distributed along the wheat genome, and polymorphic markers co-localized with genes of great agronomic importance. The geographical distribution of the inferred Bayesian clustering revealed six genetically homogenous ancestral groups among the collection, where the Central European core bared an admixed background originating from four ancestral groups. We evaluated the effective population sizes (Ne) of the Central European collection and assessed changes in diversity over time, which revealed a dramatic ~ 97% genetic erosion between 1955 and 2015.
Collapse
|
31
|
Zuo Z, Lu Y, Zhu M, Chen R, Zhang E, Hao D, Huang Q, Wang H, Su Y, Wang Z, Xu Y, Li P, Xu C, Yang Z. Nucleotide Diversity of the Maize ZmCNR13 Gene and Association With Ear Traits. Front Genet 2021; 12:773597. [PMID: 34764988 PMCID: PMC8576287 DOI: 10.3389/fgene.2021.773597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
The maize (Zea mays L.) ZmCNR13 gene, encoding a protein of fw2.2-like (FWL) family, has been demonstrated to be involved in cell division, expansion, and differentiation. In the present study, the genomic sequences of the ZmCNR13 locus were re-sequenced in 224 inbred lines, 56 landraces and 30 teosintes, and the nucleotide polymorphism and selection signature were estimated. A total of 501 variants, including 415 SNPs and 86 Indels, were detected. Among them, 51 SNPs and 4 Indels were located in the coding regions. Although neutrality tests revealed that this locus had escaped from artificial selection during the process of maize domestication, the population of inbred lines possesses lower nucleotide diversity and decay of linkage disequilibrium. To estimate the association between sequence variants of ZmCNR13 and maize ear characteristics, a total of ten ear-related traits were obtained from the selected inbred lines. Four variants were found to be significantly associated with six ear-related traits. Among them, SNP2305, a non-synonymous mutation in exon 2, was found to be associated with ear weight, ear grain weight, ear diameter and ear row number, and explained 4.59, 4.61, 4.31, and 8.42% of the phenotypic variations, respectively. These results revealed that natural variations of ZmCNR13 might be involved in ear development and can be used in genetic improvement of maize ear-related traits.
Collapse
Affiliation(s)
- Zhihao Zuo
- Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yue Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Minyan Zhu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Rujia Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Enying Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Derong Hao
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China
| | - Qianfeng Huang
- Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Hanyao Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Yanze Su
- Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Zhichao Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| |
Collapse
|
32
|
Monnot S, Desaint H, Mary-Huard T, Moreau L, Schurdi-Levraud V, Boissot N. Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances. Cells 2021; 10:3080. [PMID: 34831303 PMCID: PMC8625838 DOI: 10.3390/cells10113080] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 01/04/2023] Open
Abstract
Growing virus resistant varieties is a highly effective means to avoid yield loss due to infection by many types of virus. The challenge is to be able to detect resistance donors within plant species diversity and then quickly introduce alleles conferring resistance into elite genetic backgrounds. Until now, mainly monogenic forms of resistance with major effects have been introduced in crops. Polygenic resistance is harder to map and introduce in susceptible genetic backgrounds, but it is likely more durable. Genome wide association studies (GWAS) offer an opportunity to accelerate mapping of both monogenic and polygenic resistance, but have seldom been implemented and described in the plant-virus interaction context. Yet, all of the 48 plant-virus GWAS published so far have successfully mapped QTLs involved in plant virus resistance. In this review, we analyzed general and specific GWAS issues regarding plant virus resistance. We have identified and described several key steps throughout the GWAS pipeline, from diversity panel assembly to GWAS result analyses. Based on the 48 published articles, we analyzed the impact of each key step on the GWAS power and showcase several GWAS methods tailored to all types of viruses.
Collapse
Affiliation(s)
- Severine Monnot
- INRAE, Génétique et Amélioration des Fruits et Légumes (GAFL), 84143 Montfavet, France
- Bayer Crop Science, Chemin de Roque Martine, 13670 Saint-Andiol, France
| | - Henri Desaint
- INRAE, Génétique et Amélioration des Fruits et Légumes (GAFL), 84143 Montfavet, France
| | - Tristan Mary-Huard
- INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, Ferme du Moulon, 91190 Gif-sur-Yvette, France
- Mathématiques et Informatique Appliquées (MIA)-Paris, INRAE, AgroParisTech, Université Paris-Saclay, 75231 Paris, France
| | - Laurence Moreau
- INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, Ferme du Moulon, 91190 Gif-sur-Yvette, France
| | | | - Nathalie Boissot
- INRAE, Génétique et Amélioration des Fruits et Légumes (GAFL), 84143 Montfavet, France
| |
Collapse
|
33
|
Bhat JA, Yu D, Bohra A, Ganie SA, Varshney RK. Features and applications of haplotypes in crop breeding. Commun Biol 2021; 4:1266. [PMID: 34737387 PMCID: PMC8568931 DOI: 10.1038/s42003-021-02782-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/09/2021] [Indexed: 12/17/2022] Open
Abstract
Climate change with altered pest-disease dynamics and rising abiotic stresses threatens resource-constrained agricultural production systems worldwide. Genomics-assisted breeding (GAB) approaches have greatly contributed to enhancing crop breeding efficiency and delivering better varieties. Fast-growing capacity and affordability of DNA sequencing has motivated large-scale germplasm sequencing projects, thus opening exciting avenues for mining haplotypes for breeding applications. This review article highlights ways to mine haplotypes and apply them for complex trait dissection and in GAB approaches including haplotype-GWAS, haplotype-based breeding, haplotype-assisted genomic selection. Improvement strategies that efficiently deploy superior haplotypes to hasten breeding progress will be key to safeguarding global food security.
Collapse
Affiliation(s)
- Javaid Akhter Bhat
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Abhishek Bohra
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research (ICAR- IIPR), Kanpur, India
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, WB, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
- State Agricultural Biotechnology Centre, Centre for Crop & Food Research Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia.
| |
Collapse
|
34
|
Hu S, Wang M, Zhang X, Chen W, Song X, Fu X, Fang H, Xu J, Xiao Y, Li Y, Bai G, Li J, Yang X. Genetic basis of kernel starch content decoded in a maize multi-parent population. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2192-2205. [PMID: 34077617 PMCID: PMC8541773 DOI: 10.1111/pbi.13645] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/20/2021] [Accepted: 05/31/2021] [Indexed: 05/25/2023]
Abstract
Starch is the most abundant storage carbohydrate in maize kernels and provides calories for humans and other animals as well as raw materials for various industrial applications. Decoding the genetic basis of natural variation in kernel starch content is needed to manipulate starch quantity and quality via molecular breeding to meet future needs. Here, we identified 50 unique single quantitative trait loci (QTLs) for starch content with 18 novel QTLs via single linkage mapping, joint linkage mapping and a genome-wide association study in a multi-parent population containing six recombinant inbred line populations. Only five QTLs explained over 10% of phenotypic variation in single populations. In addition to a few large-effect and many small-effect additive QTLs, limited pairs of epistatic QTLs also contributed to the genetic basis of the variation in kernel starch content. A regional association study identified five non-starch-pathway genes that were the causal candidate genes underlying the identified QTLs for starch content. The pathway-driven analysis identified ZmTPS9, which encodes a trehalose-6-phosphate synthase in the trehalose pathway, as the causal gene for the QTL qSTA4-2, which was detected by all three statistical analyses. Knockout of ZmTPS9 increased kernel starch content and, in turn, kernel weight in maize, suggesting potential applications for ZmTPS9 in maize starch and yield improvement. These findings extend our knowledge about the genetic basis of starch content in maize kernels and provide valuable information for maize genetic improvement of starch quantity and quality.
Collapse
Affiliation(s)
- Shuting Hu
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Min Wang
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Xuan Zhang
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Wenkang Chen
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Xinran Song
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
- Agronomy CollegeXinjiang Agricultural UniversityUrumqiChina
| | - Xiuyi Fu
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
- Maize Research CenterBeijing Academy of Agriculture & Forestry Sciences (BAAFS)BeijingChina
| | - Hui Fang
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Jing Xu
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Yingni Xiao
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
- Crop Research InstituteGuangdong Academy of Agricultural SciencesKey Laboratory of Crops Genetics and Improvement of Guangdong ProvinceGuangzhouChina
| | - Yaru Li
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Guanghong Bai
- Agronomy CollegeXinjiang Agricultural UniversityUrumqiChina
| | - Jiansheng Li
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| |
Collapse
|
35
|
Wang M, Fang Z, Yoo B, Bejerano G, Peltz G. The Effect of Population Structure on Murine Genome-Wide Association Studies. Front Genet 2021; 12:745361. [PMID: 34589118 PMCID: PMC8475632 DOI: 10.3389/fgene.2021.745361] [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] [Received: 07/21/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
The ability to use genome-wide association studies (GWAS) for genetic discovery depends upon our ability to distinguish true causative from false positive association signals. Population structure (PS) has been shown to cause false positive signals in GWAS. PS correction is routinely used for analysis of human GWAS results, and it has been assumed that it also should be utilized for murine GWAS using inbred strains. Nevertheless, there are fundamental differences between murine and human GWAS, and the impact of PS on murine GWAS results has not been carefully investigated. To assess the impact of PS on murine GWAS, we examined 8223 datasets that characterized biomedical responses in panels of inbred mouse strains. Rather than treat PS as a confounding variable, we examined it as a response variable. Surprisingly, we found that PS had a minimal impact on datasets measuring responses in ≤20 strains; and had surprisingly little impact on most datasets characterizing 21 - 40 inbred strains. Moreover, we show that true positive association signals arising from haplotype blocks, SNPs or indels, which were experimentally demonstrated to be causative for trait differences, would be rejected if PS correction were applied to them. Our results indicate because of the special conditions created by GWAS (the use of inbred strains, small sample sizes) PS assessment results should be carefully evaluated in conjunction with other criteria, when murine GWAS results are evaluated.
Collapse
Affiliation(s)
- Meiyue Wang
- Department of Anesthesia, Stanford University School of Medicine, Stanford, CA, United States
| | - Zhuoqing Fang
- Department of Anesthesia, Stanford University School of Medicine, Stanford, CA, United States
| | - Boyoung Yoo
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, United States
| | - Gill Bejerano
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, United States.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, United States.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States.,Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, United States
| | - Gary Peltz
- Department of Anesthesia, Stanford University School of Medicine, Stanford, CA, United States
| |
Collapse
|
36
|
George AW, Verbyla A, Bowden J. Eagle for better genome-wide association mapping. G3-GENES GENOMES GENETICS 2021; 11:6322957. [PMID: 34544142 PMCID: PMC8496271 DOI: 10.1093/g3journal/jkab204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022]
Abstract
Eagle is an R package for multi-locus association mapping on a genome-wide scale. It is unlike other multi-locus packages in that it is easy to use for R users and non-users alike. It has two modes of use, command line and graphical user interface. Eagle is fully documented and has its own supporting website, http://eagle.r-forge.r-project.org/index.html. Eagle is a significant improvement over the method-of-choice, single-locus association mapping. It has greater power to detect SNP-trait associations. It is based on model selection, linear mixed models, and a clever idea on how random effects can be used to identify SNP-trait associations. Through an example with real mouse data, we demonstrate Eagle's ability to bring clarity and increased insight to single-locus findings. Initially, we see Eagle complementing single-locus analyses. However, over time, we hope the community will make, increasingly, multi-locus association mapping their method-of-choice for the analysis of genome-wide association study data.
Collapse
Affiliation(s)
- Andrew W George
- Data61, Commonwealth Scientific and Industrial Research Organisation, Brisbane 4102, Australia
| | - Arunas Verbyla
- Data61, Commonwealth Scientific and Industrial Research Organisation, Atherton 4883, Australia
| | - Joshua Bowden
- Inria Rennes-Bretagne Atlantique, Campus Universitaire de Beaulieu, Rennes 35042, France
| |
Collapse
|
37
|
Panahabadi R, Ahmadikhah A, McKee LS, Ingvarsson PK, Farrokhi N. Genome-Wide Association Mapping of Mixed Linkage (1,3;1,4)-β-Glucan and Starch Contents in Rice Whole Grain. FRONTIERS IN PLANT SCIENCE 2021; 12:665745. [PMID: 34512678 PMCID: PMC8424012 DOI: 10.3389/fpls.2021.665745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/28/2021] [Indexed: 05/27/2023]
Abstract
The glucan content of rice is a key factor defining its nutritional and economic value. Starch and its derivatives have many industrial applications such as in fuel and material production. Non-starch glucans such as (1,3;1,4)-β-D-glucan (mixed-linkage β-glucan, MLG) have many benefits in human health, including lowering cholesterol, boosting the immune system, and modulating the gut microbiome. In this study, the genetic variability of MLG and starch contents were analyzed in rice (Oryza sativa L.) whole grain, by performing a new quantitative analysis of the polysaccharide content of rice grains. The 197 rice accessions investigated had an average MLG content of 252 μg/mg, which was negatively correlated with the grain starch content. A new genome-wide association study revealed seven significant quantitative trait loci (QTLs) associated with the MLG content and two QTLs associated with the starch content in rice whole grain. Novel genes associated with the MLG content were a hexose transporter and anthocyanidin 5,3-O-glucosyltransferase. Also, the novel gene associated with the starch content was a nodulin-like domain. The data pave the way for a better understanding of the genes involved in determining both MLG and starch contents in rice grains and should facilitate future plant breeding programs.
Collapse
Affiliation(s)
- Rahele Panahabadi
- Department of Plant Science and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Asadollah Ahmadikhah
- Department of Plant Science and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Lauren S. McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
- Wallenberg Wood Science Centre, Stockholm, Sweden
| | - Pär K. Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Naser Farrokhi
- Department of Plant Science and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| |
Collapse
|
38
|
Genome-wide association studies: assessing trait characteristics in model and crop plants. Cell Mol Life Sci 2021; 78:5743-5754. [PMID: 34196733 PMCID: PMC8316211 DOI: 10.1007/s00018-021-03868-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 01/19/2023]
Abstract
GWAS involves testing genetic variants across the genomes of many individuals of a population to identify genotype–phenotype association. It was initially developed and has proven highly successful in human disease genetics. In plants genome-wide association studies (GWAS) initially focused on single feature polymorphism and recombination and linkage disequilibrium but has now been embraced by a plethora of different disciplines with several thousand studies being published in model and crop species within the last decade or so. Here we will provide a comprehensive review of these studies providing cases studies on biotic resistance, abiotic tolerance, yield associated traits, and metabolic composition. We also detail current strategies of candidate gene validation as well as the functional study of haplotypes. Furthermore, we provide a critical evaluation of the GWAS strategy and its alternatives as well as future perspectives that are emerging with the emergence of pan-genomic datasets.
Collapse
|
39
|
Akond Z, Ahsan MA, Alam M, Mollah MNH. Robustification of GWAS to explore effective SNPs addressing the challenges of hidden population stratification and polygenic effects. Sci Rep 2021; 11:13060. [PMID: 34158546 PMCID: PMC8219685 DOI: 10.1038/s41598-021-90774-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/12/2021] [Indexed: 11/24/2022] Open
Abstract
Genome-wide association studies (GWAS) play a vital role in identifying important genes those is associated with the phenotypic variations of living organisms. There are several statistical methods for GWAS including the linear mixed model (LMM) which is popular for addressing the challenges of hidden population stratification and polygenic effects. However, most of these methods including LMM are sensitive to phenotypic outliers that may lead the misleading results. To overcome this problem, in this paper, we proposed a way to robustify the LMM approach for reducing the influence of outlying observations using the β-divergence method. The performance of the proposed method was investigated using both synthetic and real data analysis. Simulation results showed that the proposed method performs better than both linear regression model (LRM) and LMM approaches in terms of powers and false discovery rates in presence of phenotypic outliers. On the other hand, the proposed method performed almost similar to LMM approach but much better than LRM approach in absence of outliers. In the case of real data analysis, our proposed method identified 11 SNPs that are significantly associated with the rice flowering time. Among the identified candidate SNPs, some were involved in seed development and flowering time pathways, and some were connected with flower and other developmental processes. These identified candidate SNPs could assist rice breeding programs effectively. Thus, our findings highlighted the importance of robust GWAS in identifying candidate genes.
Collapse
Affiliation(s)
- Zobaer Akond
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
- Institute of Environmental Science, University of Rajshahi, Rajshahi, 6205, Bangladesh
- Agricultural Statistics and ICT Division, Bangladesh Agricultural Research Institute (BARI), Gazipur, 1701, Bangladesh
| | - Md Asif Ahsan
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Munirul Alam
- Molecular Ecology and Metagenomic Laboratory, Infectious Diseases Division, International Centre for Diarrheal Disease Research (Icddr,b), Rajshahi, Bangladesh
| | - Md Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh.
| |
Collapse
|
40
|
Mores A, Borrelli GM, Laidò G, Petruzzino G, Pecchioni N, Amoroso LGM, Desiderio F, Mazzucotelli E, Mastrangelo AM, Marone D. Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies. Int J Mol Sci 2021; 22:5423. [PMID: 34063853 PMCID: PMC8196592 DOI: 10.3390/ijms22115423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and 'post-genomic era' technologies, will be reviewed in order to contribute to a better understanding of the complexity of host-pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.
Collapse
Affiliation(s)
- Antonia Mores
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Grazia Maria Borrelli
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | | | - Francesca Desiderio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| |
Collapse
|
41
|
Reisetter AC, Breheny P. Penalized linear mixed models for structured genetic data. Genet Epidemiol 2021; 45:427-444. [PMID: 33998038 DOI: 10.1002/gepi.22384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/19/2021] [Accepted: 03/29/2021] [Indexed: 11/12/2022]
Abstract
Many genetic studies that aim to identify genetic variants associated with complex phenotypes are subject to unobserved confounding factors arising from environmental heterogeneity. This poses a challenge to detecting associations of interest and is known to induce spurious associations when left unaccounted for. Penalized linear mixed models (LMMs) are an attractive method to correct for unobserved confounding. These methods correct for varying levels of relatedness and population structure by modeling it as a random effect with a covariance structure estimated from observed genetic data. Despite an extensive literature on penalized regression and LMMs separately, the two are rarely discussed together. The aim of this review is to do so while examining the statistical properties of penalized LMMs in the genetic association setting. Specifically, the ability of penalized LMMs to accurately estimate genetic effects in the presence of environmental confounding has not been well studied. To clarify the important yet subtle distinction between population structure and environmental heterogeneity, we present a detailed review of relevant concepts and methods. In addition, we evaluate the performance of penalized LMMs and competing methods in terms of estimation and selection accuracy in the presence of a number of confounding structures.
Collapse
Affiliation(s)
- Anna C Reisetter
- Department of Biostatistics, University of Iowa, Iowa City, Iowa, USA
| | - Patrick Breheny
- Department of Biostatistics, University of Iowa, Iowa City, Iowa, USA
| |
Collapse
|
42
|
Shikha K, Shahi JP, Vinayan MT, Zaidi PH, Singh AK, Sinha B. Genome-wide association mapping in maize: status and prospects. 3 Biotech 2021; 11:244. [PMID: 33968587 PMCID: PMC8085158 DOI: 10.1007/s13205-021-02799-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association study (GWAS) provides a robust and potent tool to retrieve complex phenotypic traits back to their underlying genetics. Maize is an excellent crop for performing GWAS due to diverse genetic variability, rapid decay of linkage disequilibrium, availability of distinct sub-populations and abundant SNP information. The application of GWAS in maize has resulted in successful identification of thousands of genomic regions associated with many abiotic and biotic stresses. Many agronomic and quality traits of maize are severely affected by such stresses and, significantly affecting its growth and productivity. To improve productivity of maize crop in countries like India which contribute only 2% to the world's total production in 2019-2020, it is essential to understand genetic complexity of underlying traits. Various DNA markers and trait associations have been revealed using conventional linkage mapping methods. However, it has achieved limited success in improving polygenic complex traits due to lower resolution of trait mapping. The present review explores the prospects of GWAS in improving yield, quality and stress tolerance in maize besides, strengths and challenges of using GWAS for molecular breeding and genomic selection. The information gathered will facilitate elucidation of genetic mechanisms of complex traits and improve efficiency of marker-assisted selection in maize breeding. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02799-4.
Collapse
Affiliation(s)
- Kumari Shikha
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| | - J. P. Shahi
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| | - M. T. Vinayan
- International Maize and Wheat Improvement Centre (CIMMYT)-Asia, ICRISAT Campus, Patancheru, Hyderabad, Telangana India
| | - P. H. Zaidi
- International Maize and Wheat Improvement Centre (CIMMYT)-Asia, ICRISAT Campus, Patancheru, Hyderabad, Telangana India
| | - A. K. Singh
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| | - B. Sinha
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| |
Collapse
|
43
|
Jasmonates and Plant Salt Stress: Molecular Players, Physiological Effects, and Improving Tolerance by Using Genome-Associated Tools. Int J Mol Sci 2021; 22:ijms22063082. [PMID: 33802953 PMCID: PMC8002660 DOI: 10.3390/ijms22063082] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/18/2022] Open
Abstract
Soil salinity is one of the most limiting stresses for crop productivity and quality worldwide. In this sense, jasmonates (JAs) have emerged as phytohormones that play essential roles in mediating plant response to abiotic stresses, including salt stress. Here, we reviewed the mechanisms underlying the activation and response of the JA-biosynthesis and JA-signaling pathways under saline conditions in Arabidopsis and several crops. In this sense, molecular components of JA-signaling such as MYC2 transcription factor and JASMONATE ZIM-DOMAIN (JAZ) repressors are key players for the JA-associated response. Moreover, we review the antagonist and synergistic effects between JA and other hormones such as abscisic acid (ABA). From an applied point of view, several reports have shown that exogenous JA applications increase the antioxidant response in plants to alleviate salt stress. Finally, we discuss the latest advances in genomic techniques for the improvement of crop tolerance to salt stress with a focus on jasmonates.
Collapse
|
44
|
Yadav CB, Tokas J, Yadav D, Winters A, Singh RB, Yadav R, Gangashetty PI, Srivastava RK, Yadav RS. Identifying Anti-Oxidant Biosynthesis Genes in Pearl Millet [ Pennisetum glaucum (L.) R. Br.] Using Genome-Wide Association Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:599649. [PMID: 34122460 PMCID: PMC8194398 DOI: 10.3389/fpls.2021.599649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/19/2021] [Indexed: 05/05/2023]
Abstract
Pearl millet [Pennisetum glaucum (L.) R Br.] is an important staple food crop in the semi-arid tropics of Asia and Africa. It is a cereal grain that has the prospect to be used as a substitute for wheat flour for celiac patients. It is an important antioxidant food resource present with a wide range of phenolic compounds that are good sources of natural antioxidants. The present study aimed to identify the total antioxidant content of pearl millet flour and apply it to evaluate the antioxidant activity of its 222 genotypes drawn randomly from the pearl millet inbred germplasm association panel (PMiGAP), a world diversity panel of this crop. The total phenolic content (TPC) significantly correlated with DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity (% inhibition), which ranged from 2.32 to 112.45% and ferric-reducing antioxidant power (FRAP) activity ranging from 21.68 to 179.66 (mg ascorbic acid eq./100 g). Genome-wide association studies (GWAS) were conducted using 222 diverse accessions and 67 K SNPs distributed across all the seven pearl millet chromosomes. Approximately, 218 SNPs were found to be strongly associated with DPPH and FRAP activity at high confidence [-log (p) > 3.0-7.4]. Furthermore, flanking regions of significantly associated SNPs were explored for candidate gene harvesting. This identified 18 candidate genes related to antioxidant pathway genes (flavanone 7-O-beta-glycosyltransferase, GDSL esterase/lipase, glutathione S-transferase) residing within or near the association signal that can be selected for further functional characterization. Patterns of genetic variability and the associated genes reported in this study are useful findings, which would need further validation before their utilization in molecular breeding for high antioxidant-containing pearl millet cultivars.
Collapse
Affiliation(s)
- Chandra Bhan Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Jayanti Tokas
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Devvart Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Ana Winters
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Ram B. Singh
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Rama Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | | | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Rattan S. Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- *Correspondence: Rattan S. Yadav
| |
Collapse
|
45
|
Talukder SK, Islam MS, Krom N, Chang J, Saha MC. Drought Responsive Putative Marker-Trait Association in Tall Fescue as Influenced by the Presence of a Novel Endophyte. FRONTIERS IN PLANT SCIENCE 2021; 12:729797. [PMID: 34745162 PMCID: PMC8565914 DOI: 10.3389/fpls.2021.729797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/22/2021] [Indexed: 05/04/2023]
Abstract
Tall fescue (Festuca arundinacea Schreb.) is one of the most important cool-season perennial obligatory outcrossing forage grasses in the United States. The production and persistence of tall fescue is significantly affected by drought in the south-central United States. Shoot-specific endophyte (Epichloë coenophiala)-infected tall fescue showed superior performance under both biotic and abiotic stress conditions. We performed a genome-wide association analysis using clonal pairs of novel endophyte AR584-positive (EP) and endophyte-free (EF) tall fescue populations consisting of 205 genotypes to identify marker-trait associations (MTAs) that contribute to drought tolerance. The experiment was performed through November 2014 to June 2018 in the field, and phenotypic data were taken on plant height, plant spread, plant vigor, and dry biomass weight under natural summer conditions of sporadic drought. Genotyping-by-sequencing of the population generated 3,597 high quality single nucleotide polymorphisms (SNPs) for further analysis. We identified 26 putative drought responsive MTAs (17 specific to EP, eight specific to EF, and one in both EP and EF populations) and nine of them (i.e., V.ep_10, S.ef_12, V.ep_27, HSV.ef_31, S.ep_30, SV.ef_32, V.ep_68, V.ef_56, and H.ef_57) were identified within 0.5 Mb region in the tall fescue genome (44.5-44.7, 75.3-75.8, 77.5-77.9 and 143.7-144.2 Mb). Using 26 MTAs, 11 tall fescue genotypes were selected for subsequent study to develop EP and EF drought tolerant tall fescue populations. Ten orthologous genes (six for EP and four for EF population) were identified in Brachypodium genome as potential candidates for drought tolerance in tall fescue, which were also earlier reported for their involvement in abiotic stress tolerance. The MTAs and candidate genes identified in this study will be useful for marker-assisted selection in improving drought tolerance of tall fescue as well opening avenue for further drought study in tall fescue.
Collapse
Affiliation(s)
- Shyamal K. Talukder
- Grass Genomics, Noble Research Institute LLC, Ardmore, OK, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Md. Shofiqul Islam
- Grass Genomics, Noble Research Institute LLC, Ardmore, OK, United States
| | - Nick Krom
- Scientific Computing, Noble Research Institute LLC, Ardmore, OK, United States
| | - Junil Chang
- Scientific Computing, Noble Research Institute LLC, Ardmore, OK, United States
| | - Malay C. Saha
- Grass Genomics, Noble Research Institute LLC, Ardmore, OK, United States
- *Correspondence: Malay C. Saha,
| |
Collapse
|
46
|
Genome-wide association study of flowering time reveals complex genetic heterogeneity and epistatic interactions in rice. Gene 2020; 770:145353. [PMID: 33333227 DOI: 10.1016/j.gene.2020.145353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/24/2020] [Accepted: 12/01/2020] [Indexed: 11/22/2022]
Abstract
Since domestication, rice has cultivated in a wide range of latitudes with different day lengths. Selection of diverse natural variations in heading date and photoperiod sensitivity is critical for adaptation of rice to different geographical environments. To unravel the genetic architecture underlying natural variation of rice flowering time, we conducted a genome wide association study (GWAS) using several association analysis strategies with a diverse worldwide collection of 529 O. sativa accessions. Heading date was investigated in three environments under long-day or short-day conditions, and photosensitivity was evaluated. By dividing the whole association panel into subpopulations and performing GWAS with both linear mixed models and multi-locus mixed-models, we revealed hundreds of significant loci harboring novel candidate genes as well as most of the known flowering time genes. In total, 127 hotspots were detected in at least two GWAS. Universal genetic heterogeneity was found across subpopulations. We further detected abundant interactions between GWAS loci, especially in indica. Functional gene families were revealed from enrichment analysis of the 127 hotspots. The results demonstrated a rich of genetic interactions in rice flowering time genes and such epistatic interactions contributed to the large portions of missing heritability in GWAS. It suggests the increased complexity of genetic heterogeneity might discount the power of increasing the sample sizes in GWAS.
Collapse
|
47
|
Khanbo S, Tangphatsornruang S, Piriyapongsa J, Wirojsirasak W, Punpee P, Klomsa-Ard P, Ukoskit K. Candidate gene association of gene expression data in sugarcane contrasting for sucrose content. Genomics 2020; 113:229-237. [PMID: 33321201 DOI: 10.1016/j.ygeno.2020.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022]
Abstract
Association mapping of gene expression data, generated from transcriptome and proteome studies, provides a means of understanding the functional significance and trait association potential of candidate genes. In this study, we applied candidate gene association mapping to validate sugarcane genes, using data from the starch and sucrose metabolism pathway, transcriptome, and proteome. We performed multiplex PCR targeted amplicon sequencing of 109 candidate genes, using NGS technology. A range of statistical models, both single-locus and multi-locus, were compared for minimization of false positives in association mapping of four sugar-related traits with different heritability. The Fixed and random model Circulating Probability Unification model effectively suppressed false positives for both low- and high-heritability traits. We identified favorable alleles of the candidate genes involved in signalling and transcriptional regulation. The results will support genetic improvement of sugarcane and may help clarify the genetic architecture of sugar-related traits.
Collapse
Affiliation(s)
- Supaporn Khanbo
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand
| | - Sithichoke Tangphatsornruang
- National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jittima Piriyapongsa
- National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Warodom Wirojsirasak
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Prapat Punpee
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Peeraya Klomsa-Ard
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand.
| |
Collapse
|
48
|
Sapkota S, Boatwright JL, Jordan K, Boyles R, Kresovich S. Identification of Novel Genomic Associations and Gene Candidates for Grain Starch Content in Sorghum. Genes (Basel) 2020; 11:E1448. [PMID: 33276449 PMCID: PMC7760202 DOI: 10.3390/genes11121448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/10/2020] [Accepted: 11/27/2020] [Indexed: 01/15/2023] Open
Abstract
Starch accumulated in the endosperm of cereal grains as reserve energy for germination serves as a staple in human and animal nutrition. Unraveling genetic control for starch metabolism is important for breeding grains with high starch content. In this study, we used a sorghum association panel with 389 individuals and 141,557 single nucleotide polymorphisms (SNPs) to fit linear mixed models (LMM) for identifying genomic regions and potential candidate genes associated with starch content. Three associated genomic regions, one in chromosome (chr) 1 and two novel associations in chr-8, were identified using combination of LMM and Bayesian sparse LMM. All significant SNPs were located within protein coding genes, with SNPs ∼ 52 Mb of chr-8 encoding a Casperian strip membrane protein (CASP)-like protein (Sobic.008G111500) and a heat shock protein (HSP) 90 (Sobic.008G111600) that were highly expressed in reproductive tissues including within the embryo and endosperm. The HSP90 is a potential hub gene with gene network of 75 high-confidence first interactors that is enriched for five biochemical pathways including protein processing. The first interactors of HSP90 also showed high transcript abundance in reproductive tissues. The candidates of this study are likely involved in intricate metabolic pathways and represent candidate gene targets for source-sink activities and drought and heat stress tolerance during grain filling.
Collapse
Affiliation(s)
- Sirjan Sapkota
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA; (J.L.B.); (K.J.); (S.K.)
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - J. Lucas Boatwright
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA; (J.L.B.); (K.J.); (S.K.)
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - Kathleen Jordan
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA; (J.L.B.); (K.J.); (S.K.)
| | - Richard Boyles
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
- Pee Dee Research and Education Center, Clemson University, Florence, SC 29506, USA
| | - Stephen Kresovich
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA; (J.L.B.); (K.J.); (S.K.)
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| |
Collapse
|
49
|
Pujar M, Gangaprasad S, Govindaraj M, Gangurde SS, Kanatti A, Kudapa H. Genome-wide association study uncovers genomic regions associated with grain iron, zinc and protein content in pearl millet. Sci Rep 2020; 10:19473. [PMID: 33173120 PMCID: PMC7655845 DOI: 10.1038/s41598-020-76230-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
Pearl millet hybrids biofortified with iron (Fe) and zinc (Zn) promise to be part of a long-term strategy to combat micronutrient malnutrition in the arid and semi-arid tropical (SAT) regions of the world. Biofortification through molecular breeding is the way forward to achieving a rapid trait-based breeding strategy. This genome-wide association study (GWAS) was conducted to identify significant marker-trait associations (MTAs) for Fe, Zn, and protein content (PC) for enhanced biofortification breeding. A diverse panel of 281 advanced inbred lines was evaluated for Fe, Zn, and PC over two seasons. Phenotypic evaluation revealed high variability (Fe: 32–120 mg kg−1, Zn: 19–87 mg kg−1, PC: 8–16%), heritability (hbs2 ≥ 90%) and significantly positive correlation among Fe, Zn and PC (P = 0.01), implying concurrent improvement. Based on the Diversity Arrays Technology (DArT) seq assay, 58,719 highly informative SNPs were filtered for association mapping. Population structure analysis showed six major genetic groups (K = 6). A total of 78 MTAs were identified, of which 18 were associated with Fe, 43 with Zn, and 17 with PC. Four SNPs viz., Pgl04_64673688, Pgl05_135500493, Pgl05_144482656, and Pgl07_101483782 located on chromosomes Pgl04 (1), Pgl05 (2) and Pgl07 (1), respectively were co-segregated for Fe and Zn. Promising genes, ‘Late embryogenesis abundant protein’, ‘Myb domain’, ‘pentatricopeptide repeat’, and ‘iron ion binding’ coded by 8 SNPs were identified. The SNPs/genes identified in the present study presents prospects for genomics assisted biofortification breeding in pearl millet.
Collapse
Affiliation(s)
- Mahesh Pujar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502 324, India.,University of Agricultural Sciences, Shivamogga, Karnataka, 577 225, India
| | - S Gangaprasad
- University of Agricultural Sciences, Shivamogga, Karnataka, 577 225, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502 324, India.
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502 324, India
| | - A Kanatti
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502 324, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502 324, India
| |
Collapse
|
50
|
Zhang F, Kang J, Long R, Yu LX, Sun Y, Wang Z, Zhao Z, Zhang T, Yang Q. Construction of high-density genetic linkage map and mapping quantitative trait loci (QTL) for flowering time in autotetraploid alfalfa (Medicago sativa L.) using genotyping by sequencing. THE PLANT GENOME 2020; 13:e20045. [PMID: 33217205 DOI: 10.1002/tpg2.20045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
Flowering time is an important agronomic trait of alfalfa (Medicago sativa L.). Managing flowering time can produce economic benefits for farmers. To understand the genetic basis of this trait, quantitative trait loci (QTL) mapping was conducted in a full-sib population that consisted of 392 individuals segregating based on flowering time. High density linkage maps were constructed using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). The linkage maps contained 3,818 SNP markers on 64 linkage groups in two parents. The average marker density was 4.33 cM for Parent 1 (P1) and 1.47 cM for Parent 2 (P2). Phenotypic data for flowering time was collected for three years at one location. Twenty-eight QTLs were identified associated with flowering time. Eleven QTLs explained more than 10% of the phenotypic variation. Among them, five main effect QTLs located on linkage group (LG) 7D of P1 and five main effect QTLs located on LG 6D of P2 were identified. Three QTLs were co-located with other QTLs. The identified linked markers to QTLs could be used for marker-assisted selection in breeding programs to develop new alfalfa varieties to modulate flowering time.
Collapse
Affiliation(s)
- Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long-Xi Yu
- Plant Germplasm Introduction and Testing Research, United States Department of Agriculture-Agricultural Research Service, Prosser, WA, USA
| | - Yan Sun
- Grassland Science Department, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhongxiang Zhao
- Cangzhou Academy of Agriculture and Forestry Sciences, Cangzhou, China
| | - Tiejun Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|