1
|
Bourke PM, Voorrips RE, Maliepaard C. Accounting for polysomic inheritance in quantitative trait loci mapping of autopolyploids. THE NEW PHYTOLOGIST 2024; 242:19-20. [PMID: 38359874 DOI: 10.1111/nph.19455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/17/2023] [Indexed: 02/17/2024]
Affiliation(s)
- Peter M Bourke
- Plant Breeding, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| |
Collapse
|
2
|
Luo Z. Mapping quantitative trait loci in autotetraploids under a genuine tetrasomic model. THE NEW PHYTOLOGIST 2024; 242:21-22. [PMID: 38359878 DOI: 10.1111/nph.19597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Affiliation(s)
- Zewei Luo
- Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, 200433, China
| |
Collapse
|
3
|
Clot CR, Vexler L, de La O Leyva-Perez M, Bourke PM, Engelen CJM, Hutten RCB, van de Belt J, Wijnker E, Milbourne D, Visser RGF, Juranić M, van Eck HJ. Identification of two mutant JASON-RELATED genes associated with unreduced pollen production in potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:79. [PMID: 38472376 PMCID: PMC10933213 DOI: 10.1007/s00122-024-04563-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/24/2024] [Indexed: 03/14/2024]
Abstract
KEY MESSAGE Multiple QTLs control unreduced pollen production in potato. Two major-effect QTLs co-locate with mutant alleles of genes with homology to AtJAS, a known regulator of meiotic spindle orientation. In diploid potato the production of unreduced gametes with a diploid (2n) rather than a haploid (n) number of chromosomes has been widely reported. Besides their evolutionary important role in sexual polyploidisation, unreduced gametes also have a practical value for potato breeding as a bridge between diploid and tetraploid germplasm. Although early articles argued for a monogenic recessive inheritance, the genetic basis of unreduced pollen production in potato has remained elusive. Here, three diploid full-sib populations were genotyped with an amplicon sequencing approach and phenotyped for unreduced pollen production across two growing seasons. We identified two minor-effect and three major-effect QTLs regulating this trait. The two QTLs with the largest effect displayed a recessive inheritance and an additive interaction. Both QTLs co-localised with genes encoding for putative AtJAS homologs, a key regulator of meiosis II spindle orientation in Arabidopsis thaliana. The function of these candidate genes is consistent with the cytological phenotype of mis-oriented metaphase II plates observed in the parental clones. The alleles associated with elevated levels of unreduced pollen showed deleterious mutation events: an exonic transposon insert causing a premature stop, and an amino acid change within a highly conserved domain. Taken together, our findings shed light on the natural variation underlying unreduced pollen production in potato and will facilitate interploidy breeding by enabling marker-assisted selection for this trait.
Collapse
Affiliation(s)
- Corentin R Clot
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Lea Vexler
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
- Teagasc, Crops Research, Oak Park, Carlow, R93 XE12, Ireland
| | | | - Peter M Bourke
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Christel J M Engelen
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Ronald C B Hutten
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
| | - José van de Belt
- Laboratory of Genetics, Wageningen University and Research, Po Box 16, 6700 AA, Wageningen, The Netherlands
| | - Erik Wijnker
- Laboratory of Genetics, Wageningen University and Research, Po Box 16, 6700 AA, Wageningen, The Netherlands
| | - Dan Milbourne
- Teagasc, Crops Research, Oak Park, Carlow, R93 XE12, Ireland
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Martina Juranić
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Herman J van Eck
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands.
| |
Collapse
|
4
|
Lau J, Gill H, Taniguti CH, Young EL, Klein PE, Byrne DH, Riera-Lizarazu O. QTL discovery for resistance to black spot and cercospora leaf spot, and defoliation in two interconnected F1 bi-parental tetraploid garden rose populations. FRONTIERS IN PLANT SCIENCE 2023; 14:1209445. [PMID: 37575936 PMCID: PMC10413565 DOI: 10.3389/fpls.2023.1209445] [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: 04/20/2023] [Accepted: 06/19/2023] [Indexed: 08/15/2023]
Abstract
Garden roses are an economically important horticultural crop worldwide, and two major fungal pathogens, black spot (Diplocarpon rosae F.A. Wolf) and cercospora leaf spot of rose (Rosisphaerella rosicola Pass.), affect both the health and ornamental value of the plant. Most studies on black spot disease resistance have focused on diploid germplasm, and little work has been performed on cercospora leaf spot resistance. With the use of newly developed software tools for autopolyploid genetics, two interconnected tetraploid garden rose F1 populations (phenotyped over the course of 3 years) were used for quantitative trait locus (QTL) analysis of black spot and cercospora leaf spot resistance as well as plant defoliation. QTLs for black spot resistance were mapped to linkage groups (LGs) 1-6. QTLs for cercospora resistance and susceptibility were found in LGs 1, 4, and 5 and for defoliation in LGs 1, 3, and 5. The major locus on LG 5 for black spot resistance coincides with the previously discovered Rdr4 locus inherited from Rosa L. 'Radbrite' (Brite Eyes™), the common parent used in these mapping populations. This work is the first report of any QTL for cercospora resistance/susceptibility in tetraploid rose germplasm and the first report of defoliation QTL in roses. A major QTL for cercospora susceptibility coincides with the black spot resistance QTL on LG 5 (Rdr4). A major cercospora resistance QTL was found on LG 1. These populations provide a genetic resource that will further the knowledge base of rose genetics as more traits are studied. Studying more traits from these populations will allow for the stacking of various QTLs for desirable traits.
Collapse
Affiliation(s)
- Jeekin Lau
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | | | | | | | | | | | - Oscar Riera-Lizarazu
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| |
Collapse
|
5
|
Wang R, Xing S, Bourke PM, Qi X, Lin M, Esselink D, Arens P, Voorrips RE, Visser RG, Sun L, Zhong Y, Gu H, Li Y, Li S, Maliepaard C, Fang J. Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:369-380. [PMID: 36333116 PMCID: PMC9884011 DOI: 10.1111/pbi.13958] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/22/2022] [Accepted: 10/31/2022] [Indexed: 05/11/2023]
Abstract
Kiwifruit (Actinidia spp) is a woody, perennial and deciduous vine. In this genus, there are multiple ploidy levels but the main cultivated cultivars are polyploid. Despite the availability of many genomic resources in kiwifruit, SNP genotyping is still a challenge given these different levels of polyploidy. Recent advances in SNP array technologies have offered a high-throughput genotyping platform for genome-wide DNA polymorphisms. In this study, we developed a high-density SNP genotyping array to facilitate genetic studies and breeding applications in kiwifruit. SNP discovery was performed by genome-wide DNA sequencing of 40 kiwifruit genotypes. The identified SNPs were stringently filtered for sequence quality, predicted conversion performance and distribution over the available Actinidia chinensis genome. A total of 134 729 unique SNPs were put on the array. The array was evaluated by genotyping 400 kiwifruit individuals. We performed a multidimensional scaling analysis to assess the diversity of kiwifruit germplasm, showing that the array was effective to distinguish kiwifruit accessions. Using a tetraploid F1 population, we constructed an integrated linkage map covering 3060.9 cM across 29 linkage groups and performed QTL analysis for the sex locus that has been identified on Linkage Group 3 (LG3) in Actinidia arguta. Finally, our dataset presented evidence of tetrasomic inheritance with partial preferential pairing in A. arguta. In conclusion, we developed and evaluated a 135K SNP genotyping array for kiwifruit. It has the advantage of a comprehensive design that can be an effective tool in genetic studies and breeding applications in this high-value crop.
Collapse
Affiliation(s)
- Ran Wang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Siyuan Xing
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Peter M. Bourke
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Xiuquan Qi
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Miaomiao Lin
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Danny Esselink
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Paul Arens
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | | | | | - Leiming Sun
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yunpeng Zhong
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Hong Gu
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yukuo Li
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Sikai Li
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Chris Maliepaard
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Jinbao Fang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| |
Collapse
|
6
|
Thérèse Navarro A, Bourke PM, van de Weg E, Clot CR, Arens P, Finkers R, Maliepaard C. Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors. Front Genet 2023; 14:1049988. [PMID: 36936433 PMCID: PMC10014611 DOI: 10.3389/fgene.2023.1049988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Linkage mapping is an approach to order markers based on recombination events. Mapping algorithms cannot easily handle genotyping errors, which are common in high-throughput genotyping data. To solve this issue, strategies have been developed, aimed mostly at identifying and eliminating these errors. One such strategy is SMOOTH, an iterative algorithm to detect genotyping errors. Unlike other approaches, SMOOTH can also be used to impute the most probable alternative genotypes, but its application is limited to diploid species and to markers heterozygous in only one of the parents. In this study we adapted SMOOTH to expand its use to any marker type and to autopolyploids with the use of identity-by-descent probabilities, naming the updated algorithm Smooth Descent (SD). We applied SD to real and simulated data, showing that in the presence of genotyping errors this method produces better genetic maps in terms of marker order and map length. SD is particularly useful for error rates between 5% and 20% and when error rates are not homogeneous among markers or individuals. With a starting error rate of 10%, SD reduced it to ∼5% in diploids, ∼7% in tetraploids and ∼8.5% in hexaploids. Conversely, the correlation between true and estimated genetic maps increased by 0.03 in tetraploids and by 0.2 in hexaploids, while worsening slightly in diploids (∼0.0011). We also show that the combination of genotype curation and map re-estimation allowed us to obtain better genetic maps while correcting wrong genotypes. We have implemented this algorithm in the R package Smooth Descent.
Collapse
|
7
|
Montanari S, Thomson S, Cordiner S, Günther CS, Miller P, Deng CH, McGhie T, Knäbel M, Foster T, Turner J, Chagné D, Espley R. High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content. FRONTIERS IN PLANT SCIENCE 2022; 13:965397. [PMID: 36247546 PMCID: PMC9555082 DOI: 10.3389/fpls.2022.965397] [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: 06/09/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Highbush blueberry (Vaccinium corymbosum, 2n = 4x = 48) is the most cultivated type of blueberry, both in New Zealand and overseas. Its perceived nutritional value is conferred by phytonutrients, particularly anthocyanins. Identifying the genetic mechanisms that control the biosynthesis of these metabolites would enable faster development of cultivars with improved fruit qualities. Here, we used recently released tools for genetic mapping in autotetraploids to build a high-density linkage map in highbush blueberry and to detect quantitative trait loci (QTLs) for fruit anthocyanin content. Genotyping was performed by target sequencing, with ∼18,000 single nucleotide polymorphism (SNP) markers being mapped into 12 phased linkage groups (LGs). Fruits were harvested when ripe for two seasons and analyzed with high-performance liquid chromatography-mass spectrometry (HPLC-MS): 25 different anthocyanin compounds were identified and quantified. Two major QTLs that were stable across years were discovered, one on LG2 and one on LG4, and the underlying candidate genes were identified. Interestingly, the presence of anthocyanins containing acylated sugars appeared to be under strong genetic control. Information gained in this study will enable the design of molecular markers for marker-assisted selection and will help build a better understanding of the genetic control of anthocyanin biosynthesis in this crop.
Collapse
Affiliation(s)
- Sara Montanari
- The New Zealand Institute for Plant and Food Research Limited, Motueka, New Zealand
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Sarah Cordiner
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Catrin S. Günther
- The New Zealand Institute for Plant and Food Research Limited, Ruakura, New Zealand
| | - Poppy Miller
- The New Zealand Institute for Plant and Food Research Limited, Te Puke, New Zealand
| | - Cecilia H. Deng
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Tony McGhie
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Mareike Knäbel
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Toshi Foster
- The New Zealand Institute for Plant and Food Research Limited, Motueka, New Zealand
| | - Janice Turner
- The New Zealand Institute for Plant and Food Research Limited, Motueka, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Richard Espley
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| |
Collapse
|
8
|
Mengist MF, Grace MH, Mackey T, Munoz B, Pucker B, Bassil N, Luby C, Ferruzzi M, Lila MA, Iorizzo M. Dissecting the genetic basis of bioactive metabolites and fruit quality traits in blueberries ( Vaccinium corymbosum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:964656. [PMID: 36119607 PMCID: PMC9478557 DOI: 10.3389/fpls.2022.964656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/26/2022] [Indexed: 06/01/2023]
Abstract
Blueberry is well-recognized as a healthy fruit with functionality derived largely from anthocyanin and chlorogenic acid. Despite their importance, no study to date has evaluated the genetic basis of these bioactives in blueberries and their relationship with fruit quality traits. Hence, to fill this gap, a mapping population including 196 F1 individuals was phenotyped for anthocyanin and chlorogenic acid concentration and fruit quality traits (titratable acidity, pH, and total soluble solids) over 3 years and data were used for QTL mapping and correlation analysis. Total soluble solids and chlorogenic acid were positively correlated with glycosylated anthocyanin and total anthocyanin, respectively, indicating that parallel selection for these traits is possible. Across all the traits, a total of 188 QTLs were identified on chromosomes 1, 2, 4, 8, 9, 11 and 12. Notably, four major regions with overlapping major-effect QTLs were identified on chromosomes 1, 2, 4 and 8, and were responsible for acylation and glycosylation of anthocyanins in a substrate and sugar donor specific manner. Through comparative transcriptome analysis, multiple candidate genes were identified for these QTLs, including glucosyltransferases and acyltransferases. Overall, the study provides the first insights into the genetic basis controlling anthocyanins accumulation and composition, chlorogenic acid and fruit quality traits, and establishes a framework to advance genetic studies and molecular breeding for anthocyanins in blueberry.
Collapse
Affiliation(s)
- Molla Fentie Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Mary H. Grace
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Ted Mackey
- Horticultural Crops Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Corvallis, OR, United States
| | - Bryan Munoz
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Boas Pucker
- Institute of Plant Biology, TU Braunschweig, Braunschweig, Germany
- BRICS, TU Braunschweig, Braunschweig, Germany
| | - Nahla Bassil
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, United States
| | - Claire Luby
- Horticultural Crops Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Corvallis, OR, United States
| | - Mario Ferruzzi
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Mary Ann Lila
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
9
|
Lau J, Young EL, Collins S, Windham MT, Klein PE, Byrne DH, Riera-Lizarazu O. Rose Rosette Disease Resistance Loci Detected in Two Interconnected Tetraploid Garden Rose Populations. FRONTIERS IN PLANT SCIENCE 2022; 13:916231. [PMID: 35873988 PMCID: PMC9302375 DOI: 10.3389/fpls.2022.916231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/25/2022] [Indexed: 05/14/2023]
Abstract
Rose rosette disease (RRD), caused by the Rose rosette emaravirus (RRV), is a major threat to the garden rose industry in the United States. There has been limited work on the genetics of host plant resistance to RRV. Two interconnected tetraploid garden rose F1 biparental mapping populations were created to develop high-quality tetraploid rose linkage maps that allowed the discovery of RRD resistance quantitative trait loci (QTLs) on linkage groups (LGs) 5, 6, and 7. These QTLs individually accounted for around 18-40% of the phenotypic variance. The locus with the greatest effect on partial resistance was found in LG 5. Most individuals with the LG 5 QTL were in the simplex configuration; however, two individuals were duplex (likely due to double reduction). Identification of resistant individuals and regions of interest can help the development of diagnostic markers for marker-assisted selection in a breeding program.
Collapse
Affiliation(s)
- Jeekin Lau
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Ellen L. Young
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Sara Collins
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Mark T. Windham
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Patricia E. Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - David H. Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Oscar Riera-Lizarazu
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| |
Collapse
|
10
|
Bao Z, Li C, Li G, Wang P, Peng Z, Cheng L, Li H, Zhang Z, Li Y, Huang W, Ye M, Dong D, Cheng Z, VanderZaag P, Jacobsen E, Bachem CWB, Dong S, Zhang C, Huang S, Zhou Q. Genome architecture and tetrasomic inheritance of autotetraploid potato. MOLECULAR PLANT 2022; 15:1211-1226. [PMID: 35733345 DOI: 10.1016/j.molp.2022.06.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/16/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Potato (Solanum tuberosum) is the most consumed non-cereal food crop. Most commercial potato cultivars are autotetraploids with highly heterozygous genomes, severely hampering genetic analyses and improvement. By leveraging the state-of-the-art sequencing technologies and polyploid graph binning, we achieved a chromosome-scale, haplotype-resolved genome assembly of a cultivated potato, Cooperation-88 (C88). Intra-haplotype comparative analyses revealed extensive sequence and expression differences in this tetraploid genome. We identified haplotype-specific pericentromeres on chromosomes, suggesting a distinct evolutionary trajectory of potato homologous centromeres. Furthermore, we detected double reduction events that are unevenly distributed on haplotypes in 1021 of 1034 selfing progeny, a feature of autopolyploid inheritance. By distinguishing maternal and paternal haplotype sets in C88, we simulated the origin of heterosis in cultivated tetraploid with a survey of 3110 tetra-allelic loci with deleterious mutations, which were masked in the heterozygous condition by two parents. This study provides insights into the genomic architecture of autopolyploids and will guide their breeding.
Collapse
Affiliation(s)
- Zhigui Bao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Canhui Li
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming 650500, China
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Pei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhen Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lin Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Zhiyang Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yuying Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wu Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mingwang Ye
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming 650500, China
| | - Daofeng Dong
- Vegetable Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhukuan Cheng
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Evert Jacobsen
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Christian W B Bachem
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Suomeng Dong
- Department of Plant Pathology and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Qian Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Peng Cheng Laboratory, Shenzhen 518055, China.
| |
Collapse
|