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Agre PA, Clark LV, Garcia-Oliveira AL, Bohar R, Adebola P, Asiedu R, Terauchi R, Asfaw A. Identification of diagnostic KASP-SNP markers for routine breeding activities in yam (Dioscorea spp.). THE PLANT GENOME 2024; 17:e20419. [PMID: 38093501 DOI: 10.1002/tpg2.20419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/16/2023] [Accepted: 11/02/2023] [Indexed: 07/02/2024]
Abstract
Maintaining genetic purity and true-to-type clone identification are important action steps in breeding programs. This study aimed to develop a universal set of kompetitive allele-specific polymerase chain reaction (KASP)-based single nucleotide polymorphism (SNP) markers for routine breeding activities. Ultra-low-density SNP markers were created using an initial set of 173,675 SNPs that were obtained from whole-genome resequencing of 333 diverse white Guinea yam (Dioscorea rotundata Poir) genotypes. From whole-genome resequencing data, 99 putative SNP markers were found and successfully converted to high-throughput KASP genotyping assays. The markers set was validated on 374 genotypes representing six yam species. Out of the 99 markers, 50 were highly polymorphic across the species and could distinguish different yam species and pedigree origins. The selected SNP markers classified the validation population based on the different yam species and identified potential duplicates within yam species. Through penalized analysis, the male parent of progenies involved in polycrosses was successfully predicted and validated. Our research was a trailblazer in validating KASP-based SNP assays for species identification, parental fingerprinting, and quality control (QC) and quality assurance (QA) in yam breeding programs.
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Affiliation(s)
- Paterne A Agre
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Lindsay V Clark
- HPCBio, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ana Luisa Garcia-Oliveira
- Excellence in Breeding (EiB), CIMMYT-ICRAF, UN Av, Nairobi, Kenya
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, Haryana, India
| | - Rajaguru Bohar
- Excellence in Breeding (EiB), CIMMYT-ICRISAT, Hyderabad, Telangana, India
| | - Patrick Adebola
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ryohei Terauchi
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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Abdelraheem A, Zhu Y, Zeng L, Stetina S, Zhang J. A genome-wide association study for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in diploid cotton (Gossypium arboreum) and resistance transfer to tetraploid Gossypium hirsutum. Mol Genet Genomics 2024; 299:30. [PMID: 38472439 DOI: 10.1007/s00438-024-02130-9] [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: 11/09/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024]
Abstract
Fusarium wilt, caused by the soilborne fungus Fusarium oxysporum f. sp. vasinfectum (FOV), is a devastating disease affecting cotton (Gossypium spp.) worldwide. Understanding the genetic basis of resistance in diploid cotton and successfully transferring the resistance to tetraploid Upland cotton (G. hirsutum) are crucial for developing resistant cotton cultivars. Although numerous studies have been conducted to investigate the genetic basis of Fusarium wilt in tetraploid cotton, little research has been conducted on diploid species. In this study, an association mapping panel consisting of 246 accessions of G. arboreum, was used to identify chromosomal regions for FOV race 4 (FOV4) resistance based on foliar disease severity ratings in four greenhouse tests. Through a genome-wide association study (GWAS) based on 7,009 single nucleotide polymorphic (SNP) markers, 24 FOV4 resistance QTLs, including three major QTLs on chromosomes A04, A06, and A11, were detected. A validation panel consisting of 97 diploid cotton accessions was employed, confirming the presence of several QTLs. Evaluation of an introgressed BC2F7 population derived from G. hirsutum/G. aridum/G. arboreum showed significant differences in disease incidence and mortality rate, as compared to susceptible and resistant controls, suggesting that the resistance in G. arboreum and/or G. aridum was transferred into Upland cotton for the first time. The identification of novel major resistance QTLs, along with the transfer of resistance from the diploid species, expands our understanding of the genomic regions involved in conferring resistance to FOV4 and contributes to the development of resilient Upland cotton cultivars.
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Affiliation(s)
- Abdelraheem Abdelraheem
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Yi Zhu
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Linghe Zeng
- USDA Agricultural Research Service Crop Genetics Research Unit, Stoneville, MS, 38776, USA
| | - Salliana Stetina
- USDA Agricultural Research Service Crop Genetics Research Unit, Stoneville, MS, 38776, USA
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
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Naveed S, Toyinbo J, Ingole H, Valavanur Shekar P, Jones M, Campbell BT, Rustgi S. Development of High-Yielding Upland Cotton Genotypes with Reduced Regrowth after Defoliation Using a Combination of Molecular and Conventional Approaches. Genes (Basel) 2023; 14:2081. [PMID: 38003024 PMCID: PMC10671241 DOI: 10.3390/genes14112081] [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: 09/30/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Cotton is an economically important crop. However, the yield gain in cotton has stagnated over the years, probably due to its narrow genetic base. The introgression of beneficial variations through conventional and molecular approaches has helped broaden its genetic base to some extent. The growth habit of cotton is one of the crucial factors that determine crop maturation time, yield, and management. This study used 44 diverse upland cotton genotypes to develop high-yielding cotton germplasm with reduced regrowth after defoliation and early maturity by altering its growth habit from perennial to somewhat annual. We selected eight top-scoring genotypes based on the gene expression analysis of five floral induction and meristem identity genes (FT, SOC1, LFY, FUL, and AP1) and used them to make a total of 587 genetic crosses in 30 different combinations of these genotypes. High-performance progeny lines were selected based on the phenotypic data on plant height, flower and boll numbers per plant, boll opening date, floral clustering, and regrowth after defoliation as surrogates of annual growth habit, collected over four years (2019 to 2022). Of the selected lines, 8×5-B3, 8×5-B4, 9×5-C1, 8×9-E2, 8×9-E3, and 39×5-H1 showed early maturity, and 20×37-K1, 20×37-K2, and 20×37-D1 showed clustered flowering, reduced regrowth, high quality of fiber, and high lint yield. In 2022, 15 advanced lines (F8/F7) from seven cross combinations were selected and sent for an increase to a Costa Rica winter nursery to be used in advanced testing and for release as germplasm lines. In addition to these breeding lines, we developed molecular resources to breed for reduced regrowth after defoliation and improved yield by converting eight expression-trait-associated SNP markers we identified earlier into a user-friendly allele-specific PCR-based assay and tested them on eight parental genotypes and an F2 population.
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Affiliation(s)
- Salman Naveed
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (J.T.); (H.I.); (P.V.S.); (M.J.)
- USDA-ARS Southern Regional Research Center, New Orleans, LA 70124, USA
| | - Johnson Toyinbo
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (J.T.); (H.I.); (P.V.S.); (M.J.)
| | - Hrishikesh Ingole
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (J.T.); (H.I.); (P.V.S.); (M.J.)
| | - Prasanna Valavanur Shekar
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (J.T.); (H.I.); (P.V.S.); (M.J.)
| | - Michael Jones
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (J.T.); (H.I.); (P.V.S.); (M.J.)
| | - B. Todd Campbell
- USDA-ARS Coastal Plains Soil, Water, and Plant Research Center, Florence, SC 29501, USA;
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (J.T.); (H.I.); (P.V.S.); (M.J.)
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Seo J, Lee JS, Shim SL, In JG, Park CS, Lee YJ, Ahn HJ. Development and authentication of Panax ginseng cv. Sunhong with high yield and multiple tolerance to heat damage, rusty roots and lodging. HORTICULTURE, ENVIRONMENT AND BIOTECHNOLOGY 2023:1-12. [PMID: 37361129 PMCID: PMC10202357 DOI: 10.1007/s13580-023-00526-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 06/28/2023]
Abstract
Ginseng (Panax ginseng) has been used as a valuable medicinal plant in Asia, and the demand for ginseng production for health functional food is increasing worldwide after the COVID-19 crisis. Although a number of cultivars have been developed to increase ginseng production, none of them were widely cultivated in Korea because they could not resist various environmental stresses while being grown in one place for at least 4 years. To address this, Sunhong was developed as a ginseng cultivar with high yield and multiple stress tolerance by pure line selection. Sunhong showed high yield and heat tolerance comparable to Yunpoong, a representative high-yielding cultivar, and exhibited 1.4 times lower prevalence of rusty roots than Yunpoong, suggesting that Sunhong can keep its high yield and quality during long-term cultivation. In addition, distinct color and lodging resistance were expected to increase the convenience of cultivation. To supply pure seeds to farmers, we also established a reliable high-throughput authentication system for Sunhong and seven ginseng cultivars through genotyping-by-sequencing (GBS) analysis. The GBS approach enabled to identify a sufficient number of informative SNPs in ginseng, a heterozygous and polyploid species. These results contribute to the improvement of yield, quality, and homogeneity, and therefore promote the ginseng industry. Supplementary Information The online version contains supplementary material available at 10.1007/s13580-023-00526-x.
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Affiliation(s)
- Jiho Seo
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
| | - Joon-Soo Lee
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
| | - Sung-Lye Shim
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
| | - Jun-Gyo In
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
| | - Chol-Soo Park
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
| | - Yong-Jae Lee
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
| | - Hee-Jun Ahn
- Korea Ginseng Research Institute, Korea Ginseng Corporation, Daejeon, 34128 Korea
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5
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Zhu Y, Thyssen GN, Abdelraheem A, Teng Z, Fang DD, Jenkins JN, McCarty JC, Wedegaertner T, Hake K, Zhang J. A GWAS identified a major QTL for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in a MAGIC population of Upland cotton and a meta-analysis of QTLs for Fusarium wilt resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2297-2312. [PMID: 35577933 DOI: 10.1007/s00122-022-04113-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 04/20/2022] [Indexed: 05/16/2023]
Abstract
A major QTL conferring resistance to Fusarium wilt race 4 in a narrow region of chromosome D02 was identified in a MAGIC population of 550 RILs of Upland cotton. Numerous studies have been conducted to investigate the genetic basis of Fusarium wilt (FW, caused by Fusarium oxysporum f. sp. vasinfectum, FOV) resistance using bi-parental and association mapping populations in cotton. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs), together with their 11 Upland cotton (Gossypium hirsutum) parents, was used to identify QTLs for FOV race 4 (FOV4) resistance. Among the parents, Acala Ultima, M-240 RNR, and Stoneville 474 were the most resistant, while Deltapine Acala 90, Coker 315, and Stoneville 825 were the most susceptible. Twenty-two MAGIC lines were consistently resistant to FOV4. Through a genome-wide association study (GWAS) based on 473,516 polymorphic SNPs, a major FOV4 resistance QTL within a narrow region on chromosomes D02 was detected, allowing identification of 14 candidate genes. Additionally, a meta-analysis of 133 published FW resistance QTLs showed a D subgenome and individual chromosome bias and no correlation between homeologous chromosome pairs. This study represents the first GWAS study using a largest genetic population and the most comprehensive meta-analysis for FW resistance in cotton. The results illustrated that 550 lines were not enough for high resolution mapping to pinpoint a candidate gene, and experimental errors in phenotyping cotton for FW resistance further compromised the accuracy and precision in QTL localization and identification of candidate genes. This study identified FOV4-resistant parents and MAGIC lines, and the first major QTL for FOV4 resistance in Upland cotton, providing useful information for developing FOV4-resistant cultivars and further genomic studies towards identification of causal genes for FOV4 resistance in cotton.
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Affiliation(s)
- Yi Zhu
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Gregory N Thyssen
- Cotton Fiber Bioscience and Cotton Chemistry and Utilization Research Units, USDA-ARS-SRRC, New Orleans, LA, USA
| | - Abdelraheem Abdelraheem
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Zonghua Teng
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, USA
| | - Johnie N Jenkins
- Crop Science Research Laboratory, USDA-ARS, Mississippi State, MS, USA
| | - Jack C McCarty
- Crop Science Research Laboratory, USDA-ARS, Mississippi State, MS, USA
| | | | | | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
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Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species. Sci Rep 2021; 11:18617. [PMID: 34545105 PMCID: PMC8452751 DOI: 10.1038/s41598-021-97689-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
Morphological identification of closely related rice species, particularly those in the Oryza AA genome group, presents major challenges and often results in cases of misidentification. Recent work by this group identified diagnostic single nucleotide polymorphic (SNP) markers specific for several rice species and subspecies based on DArTseq next-generation sequencing technology ("DArTseq"). These SNPs can be used for quality control (QC) analysis in rice breeding and germplasm maintenance programs. Here, we present the DArTseq-based diagnostic SNPs converted into Kompetitive allele-specific PCR (KASPar or KASP) assays and validation data for a subset of them; these can be used for low-cost routine genotyping quality control (QC) analysis. Of the 224 species/subspecies' diagnostic SNPs tested, 158 of them produced working KASP assays, a conversion success rate of 70%. Two validation experiments were run with 87 of the 158 SNP markers to ensure that the assays amplified, were polymorphic, and distinguished the five species/subspecies tested. Based on these validation test results, we recommend a panel of 36 SNP markers that clearly delineate O. barthii, O. glaberrima, O. longistaminata, O. sativa spp. indica and japonica. The KASP assays provide a flexible, rapid turnaround and cost-effective tool to facilitate germplasm curation and management of these four Oryza AA genome species across multiple genebanks.
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Azizi MMF, Lau HY, Abu-Bakar N. Integration of advanced technologies for plant variety and cultivar identification. J Biosci 2021. [DOI: 10.1007/s12038-021-00214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Shen Y, Wang J, Shaw RK, Yu H, Sheng X, Zhao Z, Li S, Gu H. Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli ( Brassica oleracea L. var. italica) in China. FRONTIERS IN PLANT SCIENCE 2021; 12:655254. [PMID: 34149754 PMCID: PMC8213352 DOI: 10.3389/fpls.2021.655254] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Broccoli (Brassica oleracea var. italica) is one of the most important and nutritious vegetables widely cultivated in China. In the recent four decades, several improved varieties were bred and developed by Chinese breeders. However, the efforts for improvement of broccoli are hindered by limited information of genetic diversity and genetic relatedness contained within the available germplasms. This study evaluated the genetic diversity, genetic relationship, population structure, and fingerprinting of 372 accessions of broccoli representing most of the variability of broccoli in China. Millions of SNPs were identified by whole-genome sequencing of 23 representative broccoli genotypes. Through several stringent selection criteria, a total of 1,167 SNPs were selected to characterize genetic diversity and population structure. Of these markers, 1,067 SNPs were genotyped by target sequencing (GBTS), and 100 SNPs were genotyped by kompetitive allele specific PCR (KASP) assay. The average polymorphism information content (PIC) and expected heterozygosity (gene diversity) values were 0.33 and 0.42, respectively. Diversity analysis revealed the prevalence of low to moderate genetic diversity in the broccoli accessions indicating a narrow genetic base. Phylogenetic and principal component analyses revealed that the 372 accessions could be clustered into two main groups but with weak groupings. STRUCTURE analysis also suggested the presence of two subpopulations with weak genetic structure. Analysis of molecular variance (AMOVA) identified 13% variance among populations and 87% within populations revealing very low population differentiation, which could be attributed to massive gene flow and the reproductive biology of the crop. Based on high resolving power, a set of 28 KASP markers was chosen for DNA fingerprinting of the broccoli accessions for seed authentication and varietal identification. To the best of our knowledge, this is the first comprehensive study to measure diversity and population structure of a large collection of broccoli in China and also the first application of GBTS and KASP techniques in genetic characterization of broccoli. This work broadens the understanding of diversity, phylogeny, and population structure of a large collection of broccoli, which may enhance future breeding efforts to achieve higher productivity.
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Affiliation(s)
- Yusen Shen
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiansheng Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ranjan K. Shaw
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Huifang Yu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoguang Sheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenqing Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Sujuan Li
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Ma KB, Yang SJ, Jo YS, Kang SS, Nam M. Development of Kompetitive Allele Specific PCR markers for identification of persimmon varieties using genotyping-by-sequencing. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2020.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Bernardo A, St. Amand P, Le HQ, Su Z, Bai G. Multiplex restriction amplicon sequencing: a novel next-generation sequencing-based marker platform for high-throughput genotyping. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:254-265. [PMID: 31199572 PMCID: PMC6920337 DOI: 10.1111/pbi.13192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/04/2019] [Accepted: 06/11/2019] [Indexed: 05/31/2023]
Abstract
To enable rapid selection of traits in marker-assisted breeding, markers must be technically simple, low-cost, high-throughput and randomly distributed in a genome. We developed such a technology, designated as Multiplex Restriction Amplicon Sequencing (MRASeq), which reduces genome complexity by polymerase chain reaction (PCR) amplification of amplicons flanked by restriction sites. The first PCR primers contain restriction site sequences at 3'-ends, preceded by 6-10 bases of specific or degenerate nucleotide sequences and then by a unique M13-tail sequence which serves as a binding site for a second PCR that adds sequencing primers and barcodes to allow sample multiplexing for sequencing. The sequences of restriction sites and adjacent nucleotides can be altered to suit different species. Physical mapping of MRASeq SNPs from a biparental population of allohexaploid wheat (Triticum aestivum L.) showed a random distribution of SNPs across the genome. MRASeq generated thousands of SNPs from a wheat biparental population and natural populations of wheat and barley (Hordeum vulgare L.). This novel, next-generation sequencing-based genotyping platform can be used for linkage mapping to screen quantitative trait loci (QTL), background selection in breeding and many other genetics and breeding applications of various species.
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Affiliation(s)
- Amy Bernardo
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
| | - Paul St. Amand
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
| | - Ha Quang Le
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Zhenqi Su
- Department of AgronomyKansas State UniversityManhattanKSUSA
- China Agricultural UniversityBeijingChina
| | - Guihua Bai
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
- Department of AgronomyKansas State UniversityManhattanKSUSA
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Zhang S, Cai Y, Guo J, Li K, Peng R, Liu F, Roberts JA, Miao Y, Zhang X. Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints. Evol Bioinform Online 2019; 15:1176934319889948. [PMID: 31798299 PMCID: PMC6868568 DOI: 10.1177/1176934319889948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/30/2019] [Indexed: 11/16/2022] Open
Abstract
Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.
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Affiliation(s)
- Shulin Zhang
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Yaling Cai
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Jinggong Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Kun Li
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Renhai Peng
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, China
| | - Jeremy A Roberts
- School of Biological and Marine Sciences, Faculty of Science and Engineering, University of Plymouth, Devon, UK
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Xuebin Zhang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
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12
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Evaluation of genomic selection methods for predicting fiber quality traits in Upland cotton. Mol Genet Genomics 2019; 295:67-79. [DOI: 10.1007/s00438-019-01599-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/29/2019] [Indexed: 01/25/2023]
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13
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Ryu J, Kim WJ, Im J, Kim SH, Lee KS, Jo HJ, Kim EY, Kang SY, Lee JH, Ha BK. Genotyping-by-sequencing based single nucleotide polymorphisms enabled Kompetitive Allele Specific PCR marker development in mutant Rubus genotypes. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Ali J, Aslam UM, Tariq R, Murugaiyan V, Schnable PS, Li D, Marfori-Nazarea CM, Hernandez JE, Arif M, Xu J, Li Z. Exploiting the Genomic Diversity of Rice ( Oryza sativa L.): SNP-Typing in 11 Early-Backcross Introgression-Breeding Populations. FRONTIERS IN PLANT SCIENCE 2018; 9:849. [PMID: 29988489 PMCID: PMC6024854 DOI: 10.3389/fpls.2018.00849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 05/31/2018] [Indexed: 05/24/2023]
Abstract
This study demonstrates genotyping-by-sequencing-based single-nucleotide polymorphism (SNP)-typing in 11 early-backcross introgression populations of rice (at BC1F5), comprising a set of 564 diverse introgression lines and 12 parents. Sequencing using 10 Ion Proton runs generated a total of ∼943.4 million raw reads, out of which ∼881.6 million reads remained after trimming for low-quality bases. After alignment, 794,297 polymorphic SNPs were identified, and filtering resulted in LMD50 SNPs (low missing data, with each SNP, genotyped in at least 50% of the samples) for each sub-population. Every data point was supported by actual sequencing data without any imputation, eliminating imputation-induced errors in SNP calling. Genotyping substantiated the impacts of novel breeding strategy revealing: (a) the donor introgression patterns in ILs were characteristic with variable introgression frequency in different genomic regions, attributed mainly to stringent selection under abiotic stress and (b) considerably lower heterozygosity was observed in ILs. Functional annotation revealed 426 non-synonymous deleterious SNPs present in 102 loci with a range of 1-4 SNPs per locus and 120 novel SNPs. SNP-typing this diversity panel will further assist in the development of markers supporting genomic applications in molecular breeding programs.
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Affiliation(s)
- Jauhar Ali
- International Rice Research Institute, Los Baños, Philippines
| | - Umair M. Aslam
- International Rice Research Institute, Los Baños, Philippines
- Institute of Crop Science, University of the Philippines Los Baños, Los Baños, Philippines
| | - Rida Tariq
- International Rice Research Institute, Los Baños, Philippines
- National Institute of Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | | | - Patrick S. Schnable
- Data2Bio, LLC, Ames, IA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Delin Li
- Data2Bio, LLC, Ames, IA, United States
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Corinne M. Marfori-Nazarea
- International Rice Research Institute, Los Baños, Philippines
- Institute of Crop Science, University of the Philippines Los Baños, Los Baños, Philippines
| | - Jose E. Hernandez
- Institute of Crop Science, University of the Philippines Los Baños, Los Baños, Philippines
| | - Muhammad Arif
- National Institute of Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jianlong Xu
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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15
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Hallahan BF, Fernandez-Tendero E, Fort A, Ryder P, Dupouy G, Deletre M, Curley E, Brychkova G, Schulz B, Spillane C. Hybridity has a greater effect than paternal genome dosage on heterosis in sugar beet (Beta vulgaris). BMC PLANT BIOLOGY 2018; 18:120. [PMID: 29907096 PMCID: PMC6003118 DOI: 10.1186/s12870-018-1338-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/31/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND The phenomenon of heterosis is critical to plant breeding and agricultural productivity. Heterosis occurs when F1 hybrid offspring display quantitative improvements in traits to levels that do not occur in the parents. Increasing the genome dosage (i.e. ploidy level) of F1 offspring can contribute to heterosis effects. Sugar beet (Beta vulgaris) provides a model for investigating the relative effects of genetic hybridity and genome dosage on heterosis. Sugar beet lines of different ploidy levels were crossed to generate diploid and triploid F1 offspring to investigate the effect of; (1) paternal genome dosage increase on F1 heterosis, and; (2) homozygous versus heterozygous tetraploid male parents on F1 triploid heterosis. A range of traits of agronomic and commercial importance were analyzed for the extent of heterosis effects observed in the F1 offspring. RESULTS Comparisons of parental lines to diploid (EA, EB) and triploid (EAA, EBB) F1 hybrids for total yield, root yield, and sugar yield indicated that there was no effect of paternal genome dosage increases on heterosis levels, indicating that hybridity is the main contributor to the heterosis levels observed. For all traits measured (apart from seed viability), F1 triploid hybrids derived from heterozygous tetraploid male parents displayed equivalent levels of heterosis as F1 triploid hybrids generated with homozygous tetraploid male parents, suggesting that heterosis gains in F1 triploids do not arise by simply increasing the extent of multi-locus heterozygosity in sugar beet F1 offspring. CONCLUSIONS Overall, our study indicates that; (1) increasing the paternal genome dosage does not enhance heterosis in F1 hybrids, and; (2) increasing multi-locus heterozygosity using highly heterozygous paternal genomes to generate F1 triploid hybrids does not enhance heterosis. Our findings have implications for the design of future F1 hybrid improvement programs for sugar beet.
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Affiliation(s)
- Brendan F. Hallahan
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Eva Fernandez-Tendero
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Antoine Fort
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Peter Ryder
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Gilles Dupouy
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Marc Deletre
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Edna Curley
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | | | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
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16
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Bourke PM, Voorrips RE, Visser RGF, Maliepaard C. Tools for Genetic Studies in Experimental Populations of Polyploids. FRONTIERS IN PLANT SCIENCE 2018; 9:513. [PMID: 29720992 PMCID: PMC5915555 DOI: 10.3389/fpls.2018.00513] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/04/2018] [Indexed: 05/19/2023]
Abstract
Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies also offer the promise of understanding polyploid genomes at a level which hitherto has remained elusive.
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Affiliation(s)
| | | | | | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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17
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Tan Z, Zhang Z, Sun X, Li Q, Sun Y, Yang P, Wang W, Liu X, Chen C, Liu D, Teng Z, Guo K, Zhang J, Liu D, Zhang Z. Genetic Map Construction and Fiber Quality QTL Mapping Using the CottonSNP80K Array in Upland Cotton. FRONTIERS IN PLANT SCIENCE 2018; 9:225. [PMID: 29535744 PMCID: PMC5835031 DOI: 10.3389/fpls.2018.00225] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/06/2018] [Indexed: 05/04/2023]
Abstract
Cotton fiber quality traits are controlled by multiple quantitative trait loci (QTL), and the improvement of these traits requires extensive germplasm. Herein, an Upland cotton cultivar from America, Acala Maxxa, was crossed with a local high fiber quality cultivar, Yumian 1, and 180 recombinant inbred lines (RILs) were obtained. In order to dissect the genetic basis of fiber quality differences between these parents, a genetic map containing 12116 SNP markers was constructed using the CottonSNP80K assay, which covered 3741.81 cM with an average distance of 0.31 cM between markers. Based on the genetic map and growouts in three environments, we detected a total of 104 QTL controlling fiber quality traits. Among these QTL, 25 were detected in all three environments and 35 in two environments. Meanwhile, 19 QTL clusters were also identified, and nine contained at least one stable QTL (detected in three environments for a given trait). These stable QTL or QTL clusters are priorities for fine mapping, identifying candidate genes, elaborating molecular mechanisms of fiber development, and application in cotton breeding programs by marker-assisted selection (MAS).
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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Kirungu JN, Deng Y, Cai X, Magwanga RO, Zhou Z, Wang X, Wang Y, Zhang Z, Wang K, Liu F. Simple Sequence Repeat (SSR) Genetic Linkage Map of D Genome Diploid Cotton Derived from an Interspecific Cross between Gossypium davidsonii and Gossypium klotzschianum. Int J Mol Sci 2018; 19:E204. [PMID: 29324636 PMCID: PMC5796153 DOI: 10.3390/ijms19010204] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/06/2018] [Accepted: 01/07/2018] [Indexed: 12/22/2022] Open
Abstract
The challenge in tetraploid cotton cultivars is the narrow genetic base and therefore, the bottleneck is how to obtain interspecific hybrids and introduce the germplasm directly from wild cotton to elite cultivars. Construction of genetic maps has provided insight into understanding the genome structure, interrelationships between organisms in relation to evolution, and discovery of genes that carry important agronomic traits in plants. In this study, we generated an interspecific hybrid between two wild diploid cottons, Gossypium davidsonii and Gossypium klotzschianum, and genotyped 188 F2:3 populations in order to develop a genetic map. We screened 12,560 SWU Simple Sequence Repeat (SSR) primers and obtained 1000 polymorphic markers which accounted for only 8%. A total of 928 polymorphic primers were successfully scored and only 728 were effectively linked across the 13 chromosomes, but with an asymmetrical distribution. The map length was 1480.23 cM, with an average length of 2.182 cM between adjacent markers. A high percentage of the markers on the map developed, and for the physical map of G. raimondii, exhibited highly significant collinearity, with two types of duplication. High level of segregation distortion was observed. A total of 27 key genes were identified with diverse roles in plant hormone signaling, development, and defense reactions. The achievement of developing the F2:3 population and its genetic map constructions may be a landmark in establishing a new tool for the genetic improvement of cultivars from wild plants in cotton. Our map had an increased recombination length compared to other maps developed from other D genome cotton species.
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Affiliation(s)
- Joy Nyangasi Kirungu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yanfeng Deng
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
- School of Biological and Physical Sciences (SBPS), Main Campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Main Campus, P.O. Box 210-40601 Bondo, Kenya.
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhenmei Zhang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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Ulloa M, Hulse-Kemp AM, De Santiago LM, Stelly DM, Burke JJ. Insights Into Upland Cotton ( Gossypium hirsutum L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents. GENOMICS INSIGHTS 2017; 10:1178631017735104. [PMID: 29308012 PMCID: PMC5751910 DOI: 10.1177/1178631017735104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 09/10/2017] [Indexed: 11/17/2022]
Abstract
High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, eg, upland cotton (Gossypium hirsutum L., "2n = 52"). Three independently developed intraspecific upland mapping populations were analyzed to generate 3 high-density genetic linkage single-nucleotide polymorphism (SNP) maps and a consensus map using the CottonSNP63K array. The populations consisted of a previously reported F2, a recombinant inbred line (RIL), and reciprocal RIL population, from "Phytogen 72" and "Stoneville 474" cultivars. The cluster file provided 7417 genotyped SNP markers, resulting in 26 linkage groups corresponding to the 26 chromosomes (c) of the allotetraploid upland cotton (AD)1 arisen from the merging of 2 genomes ("A" Old World and "D" New World). Patterns of chromosome-specific recombination were largely consistent across mapping populations. The high-density genetic consensus map included 7244 SNP markers that spanned 3538 cM and comprised 3824 SNP bins, of which 1783 and 2041 were in the At and Dt subgenomes with 1825 and 1713 cM map lengths, respectively. Subgenome average distances were nearly identical, indicating that subgenomic differences in bin number arose due to the high numbers of SNPs on the Dt subgenome. Examination of expected recombination frequency or crossovers (COs) on the chromosomes within each population of the 2 subgenomes revealed that COs were also not affected by the SNPs or SNP bin number in these subgenomes. Comparative alignment analyses identified historical ancestral At-subgenomic translocations of c02 and c03, as well as of c04 and c05. The consensus map SNP sequences aligned with high congruency to the NBI assembly of Gossypium hirsutum. However, the genomic comparisons revealed evidence of additional unconfirmed possible duplications, inversions and translocations, and unbalance SNP sequence homology or SNP sequence/loci genomic dominance, or homeolog loci bias of the upland tetraploid At and Dt subgenomes. The alignments indicated that 364 SNP-associated previously unintegrated scaffolds can be placed in pseudochromosomes of the NBI G hirsutum assembly. This is the first intraspecific SNP genetic linkage consensus map assembled in G hirsutum with a core of reproducible mendelian SNP markers assayed on different populations and it provides further knowledge of chromosome arrangement of genic and nongenic SNPs. Together, the consensus map and RIL populations provide a synergistically useful platform for localizing and identifying agronomically important loci for improvement of the cotton crop.
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Affiliation(s)
- Mauricio Ulloa
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, USA
| | - Amanda M Hulse-Kemp
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Luis M De Santiago
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX, USA
| | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - John J Burke
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, USA
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20
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Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC PLANT BIOLOGY 2017; 17:37. [PMID: 28158969 PMCID: PMC5291959 DOI: 10.1186/s12870-017-0981-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/23/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. RESULTS The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. CONCLUSIONS Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.
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Affiliation(s)
- Lori L. Hinze
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - Amanda M. Hulse-Kemp
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Iain W. Wilson
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Danny J. Llewellyn
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Jen M. Taylor
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Andrew Spriggs
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - David D. Fang
- USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA 70124 USA
| | - Mauricio Ulloa
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - John J. Burke
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398 France
- EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO Brazil
| | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Jodi A. Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS 38776 USA
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
| | | | - Cindy T. Lawley
- Illumina Inc., 499 Illinois Street, San Francisco, CA 94158 USA
| | - Don C. Jones
- Cotton Incorporated, Agricultural Research, Cary, NC 27513 USA
| | - Richard G. Percy
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - David M. Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
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21
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Islam MS, Thyssen GN, Jenkins JN, Zeng L, Delhom CD, McCarty JC, Deng DD, Hinchliffe DJ, Jones DC, Fang DD. A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton. BMC Genomics 2016; 17:903. [PMID: 27829353 PMCID: PMC5103610 DOI: 10.1186/s12864-016-3249-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/02/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Cotton supplies a great majority of natural fiber for the global textile industry. The negative correlation between yield and fiber quality has hindered breeders' ability to improve these traits simultaneously. A multi-parent advanced generation inter-cross (MAGIC) population developed through random-mating of multiple diverse parents has the ability to break this negative correlation. Genotyping-by-sequencing (GBS) is a method that can rapidly identify and genotype a large number of single nucleotide polymorphisms (SNP). Genotyping a MAGIC population using GBS technologies will enable us to identify marker-trait associations with high resolution. RESULTS An Upland cotton MAGIC population was developed through random-mating of 11 diverse cultivars for five generations. In this study, fiber quality data obtained from four environments and 6071 SNP markers generated via GBS and 223 microsatellite markers of 547 recombinant inbred lines (RILs) of the MAGIC population were used to conduct a genome wide association study (GWAS). By employing a mixed linear model, GWAS enabled us to identify markers significantly associated with fiber quantitative trait loci (QTL). We identified and validated one QTL cluster associated with four fiber quality traits [short fiber content (SFC), strength (STR), length (UHM) and uniformity (UI)] on chromosome A07. We further identified candidate genes related to fiber quality attributes in this region. Gene expression and amino acid substitution analysis suggested that a regeneration of bulb biogenesis 1 (GhRBB1_A07) gene is a candidate for superior fiber quality in Upland cotton. The DNA marker CFBid0004 designed from an 18 bp deletion in the coding sequence of GhRBB1_A07 in Acala Ultima is associated with the improved fiber quality in the MAGIC RILs and 105 additional commercial Upland cotton cultivars. CONCLUSION Using GBS and a MAGIC population enabled more precise fiber QTL mapping in Upland cotton. The fiber QTL and associated markers identified in this study can be used to improve fiber quality through marker assisted selection or genomic selection in a cotton breeding program. Target manipulation of the GhRBB1_A07 gene through biotechnology or gene editing may potentially improve cotton fiber quality.
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Affiliation(s)
- Md Sariful Islam
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124 USA
| | - Gregory N. Thyssen
- Cotton Chemistry and Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124 USA
| | - Johnie N. Jenkins
- Genetics & Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS 39762 USA
| | - Linghe Zeng
- Crop Genetics Research Unit, USDA-ARS, Stoneville, MS 38772 USA
| | - Christopher D. Delhom
- Cotton Structure and Quality Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124 USA
| | - Jack C. McCarty
- Genetics & Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS 39762 USA
| | - Dewayne D. Deng
- Genetics & Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS 39762 USA
| | - Doug J. Hinchliffe
- Cotton Chemistry and Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124 USA
| | | | - David D. Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124 USA
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Kottapalli P, Ulloa M, Kottapalli KR, Payton P, Burke J. SNP Marker Discovery in Pima Cotton ( Gossypium barbadense L.) Leaf Transcriptomes. GENOMICS INSIGHTS 2016; 9:51-60. [PMID: 27721653 PMCID: PMC5049682 DOI: 10.4137/gei.s40377] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 11/17/2022]
Abstract
The objective of this study was to explore the known narrow genetic diversity and discover single-nucleotide polymorphic (SNP) markers for marker-assisted breeding within Pima cotton (Gossypium barbadense L.) leaf transcriptomes. cDNA from 25-day plants of three diverse cotton genotypes [Pima S6 (PS6), Pima S7 (PS7), and Pima 3-79 (P3-79)] was sequenced on Illumina sequencing platform. A total of 28.9 million reads (average read length of 138 bp) were generated by sequencing cDNA libraries of these three genotypes. The de novo assembly of reads generated transcriptome sets of 26,369 contigs for PS6, 25,870 contigs for PS7, and 24,796 contigs for P3-79. A Pima leaf reference transcriptome was generated consisting of 42,695 contigs. More than 10,000 single-nucleotide polymorphisms (SNPs) were identified between the genotypes, with 100% SNP frequency and a minimum of eight sequencing reads. The most prevalent SNP substitutions were C-T and A-G in these cotton genotypes. The putative SNPs identified can be utilized for characterizing genetic diversity, genotyping, and eventually in Pima cotton breeding through marker-assisted selection.
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Affiliation(s)
- Pratibha Kottapalli
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, USA
| | - Mauricio Ulloa
- USDA-ARS, PA, CSRL, Plant Stress and Germplasm Development Research, Lubbock, TX, USA
| | | | - Paxton Payton
- USDA-ARS, PA, CSRL, Plant Stress and Germplasm Development Research, Lubbock, TX, USA
| | - John Burke
- USDA-ARS, PA, CSRL, Plant Stress and Germplasm Development Research, Lubbock, TX, USA
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23
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Li C, Dong Y, Zhao T, Li L, Li C, Yu E, Mei L, Daud MK, He Q, Chen J, Zhu S. Genome-Wide SNP Linkage Mapping and QTL Analysis for Fiber Quality and Yield Traits in the Upland Cotton Recombinant Inbred Lines Population. FRONTIERS IN PLANT SCIENCE 2016; 7:1356. [PMID: 27660632 PMCID: PMC5014859 DOI: 10.3389/fpls.2016.01356] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/25/2016] [Indexed: 05/18/2023]
Abstract
It is of significance to discover genes related to fiber quality and yield traits and tightly linked markers for marker-assisted selection (MAS) in cotton breeding. In this study, 188 F8 recombinant inbred lines (RILs), derived from a intraspecific cross between HS46 and MARCABUCAG8US-1-88 were genotyped by the cotton 63K single nucleotide polymorphism (SNP) assay. Field trials were conducted in Sanya, Hainan Province, during the 2014-2015 cropping seasons under standard conditions. Results revealed significant differences (P < 0.05) among RILs, environments and replications for fiber quality and yield traits. Broad-sense heritabilities of all traits including fiber length, fiber uniformity, micronaire, fiber elongation, fiber strength, boll weight, and lint percentage ranged from 0.26 to 0.66. A 1784.28 cM (centimorgans) linkage map, harboring 2618 polymorphic SNP markers, was constructed, which had 0.68 cM per marker density. Seventy-one quantitative trait locus (QTLs) for fiber quality and yield traits were detected on 21 chromosomes, explaining 4.70∼32.28% phenotypic variance, in which 16 were identified as stable QTLs across two environments. Meanwhile, 12 certain regions were investigated to be involved in the control of one (hotspot) or more (cluster) traits, mainly focused on Chr05, Chr09, Chr10, Chr14, Chr19, and Chr20. Nineteen pairs of epistatic QTLs (e-QTLs) were identified, of which two pairs involved in two additive QTLs. These additive QTLs, e-QTLs, and QTL clusters were tightly linked to SNP markers, which may serve as target regions for map-based cloning, gene discovery, and MAS in cotton breeding.
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Affiliation(s)
- Cong Li
- Department of Agronomy, Zhejiang UniversityHangzhou, China
| | - Yating Dong
- Department of Agronomy, Zhejiang UniversityHangzhou, China
| | - Tianlun Zhao
- Department of Agronomy, Zhejiang UniversityHangzhou, China
| | - Ling Li
- Department of Agronomy, Zhejiang UniversityHangzhou, China
| | - Cheng Li
- Department of Agronomy, Zhejiang UniversityHangzhou, China
| | - En Yu
- Department of Agronomy, Zhejiang UniversityHangzhou, China
| | - Lei Mei
- Department of Agronomy, Zhejiang UniversityHangzhou, China
| | - M. K. Daud
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and TechnologyKohat, Pakistan
| | - Qiuling He
- Department of Agronomy, Zhejiang UniversityHangzhou, China
| | - Jinhong Chen
- Department of Agronomy, Zhejiang UniversityHangzhou, China
| | - Shuijin Zhu
- Department of Agronomy, Zhejiang UniversityHangzhou, China
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24
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Ashrafi H, Hulse-Kemp AM, Wang F, Yang SS, Guan X, Jones DC, Matvienko M, Mockaitis K, Chen ZJ, Stelly DM, Van Deynze A. A Long-Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery. THE PLANT GENOME 2015; 8:eplantgenome2014.10.0068. [PMID: 33228299 DOI: 10.3835/plantgenome2014.10.0068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/17/2015] [Indexed: 06/11/2023]
Abstract
Upland cotton (Gossypium hirsutum L.) has a narrow germplasm base, which constrains marker development and hampers intraspecific breeding. A pressing need exists for high-throughput single nucleotide polymorphism (SNP) markers that can be readily applied to germplasm in breeding and breeding-related research programs. Despite progress made in developing new sequencing technologies during the past decade, the cost of sequencing remains substantial when one is dealing with numerous samples and large genomes. Several strategies have been proposed to lower the cost of sequencing for multiple genotypes of large-genome species like cotton, such as transcriptome sequencing and reduced-representation DNA sequencing. This paper reports the development of a transcriptome assembly of the inbred line Texas Marker-1 (TM-1), a genetic standard for cotton, its usefulness as a reference for RNA sequencing (RNA-seq)-based SNP identification, and the availability of transcriptome sequences of four other cotton cultivars. An assembly of TM-1 was made using Roche 454 transcriptome reads combined with an assembly of all available public expressed sequence tag (EST) sequences of TM-1. The TM-1 assembly consists of 72,450 contigs with a total of 70 million bp. Functional predictions of the transcripts were estimated by alignment to selected protein databases. Transcriptome sequences of the five lines, including TM-1, were obtained using an Illumina Genome Analyzer-II, and the short reads were mapped to the TM-1 assembly to discover SNPs among the five lines. We identified >14,000 unfiltered allelic SNPs, of which ∼3,700 SNPs were retained for assay development after applying several rigorous filters. This paper reports availability of the reference transcriptome assembly and shows its utility in developing intraspecific SNP markers in upland cotton.
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Affiliation(s)
- Hamid Ashrafi
- Univ. of California-Davis, Dep. of Plant Sciences and Seed Biotechnology Center, One Shields Ave., Davis, CA, 95616
| | | | - Fei Wang
- Texas A&M Univ., Dep. of Soil and Crop Sciences, College Station, TX, 77843
| | - S Samuel Yang
- Texas A&M Univ., Dep. of Soil and Crop Sciences, College Station, TX, 77843
| | - Xueying Guan
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The Univ. of Texas at Austin, Austin, TX, 78712
| | | | - Marta Matvienko
- Univ. of California-Davis, Genome Center, One Shields Ave., Davis, CA, 95616
| | | | - Z Jeffrey Chen
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The Univ. of Texas at Austin, Austin, TX, 78712
| | - David M Stelly
- Texas A&M Univ., Dep. of Soil and Crop Sciences, College Station, TX, 77843
| | - Allen Van Deynze
- Univ. of California-Davis, Dep. of Plant Sciences and Seed Biotechnology Center, One Shields Ave., Davis, CA, 95616
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