Genome-wide association mapping for agronomic traits in an 8-way Upland cotton MAGIC population by SLAF-seq.
Journal
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
ISSN: 1432-2242
Titre abrégé: Theor Appl Genet
Pays: Germany
ID NLM: 0145600
Informations de publication
Date de publication:
Aug 2021
Aug 2021
Historique:
received:
01
09
2020
accepted:
12
04
2021
pubmed:
30
4
2021
medline:
1
10
2021
entrez:
29
4
2021
Statut:
ppublish
Résumé
One sub-MAGIC population was genotyped using SLAF-seq, and QTLs and candidate genes for agronomic traits were identified in Upland cotton. The agronomic traits of Upland cotton have serious impacts on cotton production, as well as economic benefits. To discover the genetic basis of important agronomic traits in Upland cotton, a subset MAGIC (multi-parent advanced generation inter-cross) population containing 372 lines (SMLs) was selected from an 8-way MAGIC population with 960 lines. The 372 lines and 8 parents were phenotyped in six environments and deeply genotyped by SLAF-seq with 60,495 polymorphic SNPs. The genetic diversity indexes of all SNPs were 0.324 and 0.362 for the parents and MAGIC lines, respectively. The LD decay distance of the SMLs was 600 kb (r
Identifiants
pubmed: 33912997
doi: 10.1007/s00122-021-03835-w
pii: 10.1007/s00122-021-03835-w
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2459-2468Subventions
Organisme : National Natural Science Foundation of China
ID : 31371674
Informations de copyright
© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Références
Abdurakhmonov IY, Kohel RJ, Yu JZ, Pepper AE, Abdullaev AA, Kushanov FN, Salakhutdinov IB, Buriev ZT, Saha S, Scheffler BE, Jenkins JN, Abdukarimov A (2008) Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics 92:478–487
pubmed: 18801424
doi: 10.1016/j.ygeno.2008.07.013
pmcid: 18801424
Abdurakhmonov IY, Saha S, Jenkins JN, Buriev ZT, Shermatov SE, Scheffler BE, Pepper AE, Yu JZ, Kohel RJ, Abdukarimov A (2009) Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica 136:401–417
pubmed: 19067183
doi: 10.1007/s10709-008-9337-8
pmcid: 19067183
Abdurakhmonov IY, Buriev ZT, Saha S, Jenkins JN, Abdukarimov A, Pepper AE (2014) Phytochrome RNAi enhances major fibre quality and agronomic traits of the cotton Gossypium hirsutum L. Nature commun 5:3062
doi: 10.1038/ncomms4062
Argiriou A, Kalivas A, Michailidis G, Tsaftaris A (2012) Characterization of PROFILIN genes from allotetraploid (Gossypium hirsutum) cotton and its diploid progenitors and expression analysis in cotton genotypes differing in fiber characteristics. Mol Biol Rep 39:3523–3532
pubmed: 21725637
doi: 10.1007/s11033-011-1125-3
pmcid: 21725637
Bai WQ, Xiao YH, Zhao J, Song SQ, Hu L, Zeng JY, Li XB, Hou L, Luo M, Li DM, Pei Y (2014) Gibberellin overproduction promotes sucrose synthase expression and secondary cell wall deposition in cotton fibers. PLoS ONE 9:e96537
pubmed: 24816840
pmcid: 4015984
doi: 10.1371/journal.pone.0096537
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635
pubmed: 17586829
pmcid: 17586829
doi: 10.1093/bioinformatics/btm308
Cai C, Ye W, Zhang T, Guo W (2014) Association analysis of fiber quality traits and exploration of elite alleles in Upland cotton cultivars/accessions (Gossypium hirsutum L.). J Integr Plant Biol 56:51–62
pubmed: 24428209
doi: 10.1111/jipb.12124
pmcid: 24428209
Chen ZJ, Scheffler BE, Dennis E, Triplett BA, Zhang T, Guo W, Chen X, Stelly DM, Rabinowicz PD, Town CD, Arioli T, Brubaker C, Cantrell RG, Lacape JM, Ulloa M, Chee P, Gingle AR, Haigler CH, Percy R, Saha S, Wilkins T, Wright RJ, Van Deynze A, Zhu Y, Yu S, Abdurakhmonov I, Katageri I, Kumar PA, Mehboob Ur R, Zafar Y, Yu JZ, Kohel RJ, Wendel JF, Paterson AH (2007) Toward sequencing cotton (Gossypium) genomes. Plant Physiol 145:1303–1310
pubmed: 18056866
pmcid: 2151711
doi: 10.1104/pp.107.107672
Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510
pubmed: 21681211
pmcid: 21681211
doi: 10.1038/nrg3012
Fang X, Liu X, Wang X, Wang W, Liu D, Zhang J, Liu D, Teng Z, Tan Z, Liu F, Zhang F, Jiang M, Jia X, Zhong J, Yang J, Zhang Z (2017) Fine-mapping qFS07.1 controlling fiber strength in upland cotton (Gossypium hirsutum L.). Theor Appl Genet 130:795–806
pubmed: 28144698
doi: 10.1007/s00122-017-2852-1
pmcid: 28144698
Flint-Garcia SA, Thornsberry JM, Buckler ESt, (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374
pubmed: 14502995
pmcid: 14502995
doi: 10.1146/annurev.arplant.54.031902.134907
Frankham R (1996) Introduction to quantitative genetics edition. Trends Genet. 12(7), 280
Handi SS, Katageri IS, Adiger S, Jadhav MP, Lekkala SP, Reddy Lachagari VB, Jenkins J (2017) Association mapping for seed cotton yield, yield components and fibre quality traits in upland cotton (Gossypium hirsutum L.) genotypes. Plant Breed 136:958–968
doi: 10.1111/pbr.12536
Hardy OJ, Vekemans X (2002) SPAGEDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620
doi: 10.1046/j.1471-8286.2002.00305.x
Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q, Li W, Guo Y, Deng L, Zhu C, Fan D, Lu Y, Weng Q, Liu K, Zhou T, Jing Y, Si L, Dong G, Huang T, Lu T, Feng Q, Qian Q, Li J, Han B (2012) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44:32–39
doi: 10.1038/ng.1018
Huang BE, Verbyla KL, Verbyla AP, Raghavan C, Singh VK, Gaur P, Leung H, Varshney RK, Cavanagh CR (2015) MAGIC populations in crops: current status and future prospects. Theor Appl Genet 128:999–1017
pubmed: 25855139
doi: 10.1007/s00122-015-2506-0
pmcid: 25855139
Huang C, Nie X, Shen C, You C, Li W, Zhao W, Zhang X, Lin Z (2017) Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs. Plant Biotechnol J 15:1374–1386
pubmed: 28301713
pmcid: 5633765
doi: 10.1111/pbi.12722
Huang C, Shen C, Wen T, Gao B, Zhu D, Li X, Ahmed MM, Li D, Lin Z (2018) SSR-based association mapping of fiber quality in upland cotton using an 8-way MAGIC population. Mol Genet Genom 293:793–805
doi: 10.1007/s00438-018-1419-4
Huang C, Li X, Li D, Lin Z (2018) QTL mapping for yield, growth period and plant height traits in upland cotton using MAGIC population. Acta Agron Sin 44(9):1320–1333
doi: 10.3724/SP.J.1006.2018.01320
Islam MS, Thyssen GN, Jenkins JN, Zeng L, Delhom CD, McCarty JC, Deng DD, Hinchliffe DJ, Jones DC, Fang DD (2016) A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton. BMC Genom 17:903
doi: 10.1186/s12864-016-3249-2
Joukhadar R, Hollaway G, Shi F, Kant S, Forrest K, Wong D, Petkowski J, Pasam R, Tibbits J, Bariana H, Bansal U, Spangenberg G, Daetwyler H, Gendall T, Hayden M (2020) Genome-wide association reveals a complex architecture for rust resistance in 2300 worldwide bread wheat accessions screened under various Australian conditions. Theor Appl Genet 133:2695–2712
pubmed: 32504212
doi: 10.1007/s00122-020-03626-9
pmcid: 32504212
Letunic I, Bork P (2016) Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 44:W242-245
pubmed: 27095192
pmcid: 4987883
doi: 10.1093/nar/gkw290
Li XB, Fan XP, Wang XL, Cai L, Yang WC (2005) The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation. Plant Cell 17:859–875
pubmed: 15722467
pmcid: 1069704
doi: 10.1105/tpc.104.029629
Li X, Jin X, Wang H, Zhang X, Lin Z (2016) Structure, evolution, and comparative genomics of tetraploid cotton based on a high-density genetic linkage map. DNA Res 3:283–293
doi: 10.1093/dnares/dsw016
Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129
pubmed: 15705655
pmcid: 15705655
doi: 10.1093/bioinformatics/bti282
Liu ZH, Zhu L, Shi HY, Chen Y, Zhang JM, Zheng Y, Li XB (2013) Cotton GASL genes encoding putative gibberellin-regulated proteins are involved in response to GA signaling in fiber development. Mol Biol Rep 40:4561–4570
pubmed: 23645033
doi: 10.1007/s11033-013-2543-1
pmcid: 23645033
Machado A, Wu Y, Yang Y, Llewellyn DJ, Dennis ES (2009) The MYB transcription factor GhMYB25 regulates early fibre and trichome development. Plant J 59:52–62
pubmed: 19309462
doi: 10.1111/j.1365-313X.2009.03847.x
pmcid: 19309462
Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12:57–63
pubmed: 17224302
doi: 10.1016/j.tplants.2006.12.001
pmcid: 17224302
Naoumkina M, Thyssen GN, Fang DD, Jenkins JN, Mccarty JC, Florane CB (2019) Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population. BMC Genom 20(1):119
doi: 10.1186/s12864-019-5427-5
Nie X, Huang C, You C, Li W, Zhao W, Shen C, Zhang B, Wang H, Yan Z, Dai B, Wang M, Zhang X, Lin Z (2016) Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China. BMC Genom 17:352
doi: 10.1186/s12864-016-2662-x
Qin H, Chen M, Yi X, Bie S, Zhang C, Zhang Y, Lan J, Meng Y, Yuan Y, Jiao C (2015) Identification of associated SSR markers for yield component and fiber quality traits based on frame map and Upland cotton collections. PLoS ONE 10:e0118073
pubmed: 25635680
pmcid: 4311988
doi: 10.1371/journal.pone.0118073
Su J, Pang C, Wei H, Li L, Liang B, Wang C, Song M, Wang H, Zhao S, Jia X, Mao G, Huang L, Geng D, Wang C, Fan S, Yu S (2016) Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton. BMC Genom 17:687
doi: 10.1186/s12864-016-2875-z
Su J, Li L, Pang C, Wei H, Wang C, Song M, Wang H, Zhao S, Zhang C, Mao G, Huang L, Wang C, Fan S, Yu S (2016) Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection. Sci Rep 6:38496
pubmed: 27924947
pmcid: 5141495
doi: 10.1038/srep38496
Su J, Fan S, Li L, Wei H, Wang C, Wang H, Song M, Zhang C, Gu L, Zhao S, Mao G, Wang C, Pang C, Yu S (2016) Detection of favorable QTL alleles and candidate genes for lint percentage by GWAS in Chinese Upland Cotton. Front Plant Sci 7:1576
pubmed: 27818672
pmcid: 5073211
Su X, Zhu G, Song X, Xu H, Li W, Ning X, Chen Q, Guo W (2020) Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense). BMC Plant Biol 20:289
pubmed: 32571222
pmcid: 7310526
doi: 10.1186/s12870-020-02502-4
Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, Jiang C, Guan N, Ma C, Zeng H, Xu C, Song J, Huang L, Wang C, Shi J, Wang R, Zheng X, Lu CY, Wang X, Zheng H (2013) SLAF-seq: An efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS ONE 8:e58700
pubmed: 23527008
pmcid: 3602454
doi: 10.1371/journal.pone.0058700
Sun Z, Wang X, Liu Z, Gu Q, Zhan Y, Li Z, Ke H, Yang J, Wu J, Wu L, Zhang G, Zhang C, Ma Z (2017) Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L. Plant Biotech J 15:982–996
doi: 10.1111/pbi.12693
Tang W, Tu L, Yang X, Tan J, Deng F, Hao J, Guo K, Lindsey K, Zhang X (2014) The calcium sensor GhCaM7 promotes cotton fiber elongation by modulating reactive oxygen species (ROS) production. New Phytol 202:509–520
pubmed: 24443839
doi: 10.1111/nph.12676
pmcid: 24443839
Wang M, Yan J, Zhao J, Song W, Zhang X, Xiao Y, Zheng Y (2012) Genome-wide association study (GWAS) of resistance to head smut in maize. Plant Sci 196:125–131
pubmed: 23017907
doi: 10.1016/j.plantsci.2012.08.004
pmcid: 23017907
Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, Ye Z, Shen C, Li J, Zhang L, Zhou X, Nie X, Li Z, Guo K, Ma Y, Huang C, Jin S, Zhu L, Yang X, Min L, Yuan D, Zhang Q, Lindsey K, Zhang X (2017) Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet 49:579–587
pubmed: 28263319
doi: 10.1038/ng.3807
pmcid: 28263319
Wang M, Tu L, Yuan D, Zhu D, Shen C, Li J, Liu F, Pei L, Wang P, Zhao G, Ye Z, Huang H, Yan F, Ma Y, Zhang L, Liu M, You J, Yang Y, Liu Z, Huang F, Li B, Qiu P, Zhang Q, Zhu L, Jin S, Yang X, Min L, Li G, Chen LL, Zheng H, Lindsey K, Lin Z, Udall JA, Zhang X (2019) Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nat Genet 51:224–229
pubmed: 30510239
doi: 10.1038/s41588-018-0282-x
pmcid: 30510239
Wen T, Wu M, Shen C, Gao B, Zhu ZX, You C, Lin Z (2018) Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum). Plant Biotech J 16:1654–1666
doi: 10.1111/pbi.12902
Wendel JF, Grover CE (2015) Taxonomy and evolution of the cotton genus. John Wiley & Sons Ltd, Gossypium Cotton
Wubben M, Thyssen G, Callahan F, Fang D, Jenkins J (2019) A novel variant of Gh_D02G0276 is required for root-knot nematode resistance on chromosome 14 (D02) in Upland cotton. Theor Appl Genet 132:1425–1434
pubmed: 30741320
doi: 10.1007/s00122-019-03289-1
pmcid: 30741320
Xiao Y, Tong H, Yang X, Xu S, Pan Q, Qiao F, Raihan MS, Luo Y, Liu H, Zhang X, Yang N, Wang X, Deng M, Jin M, Zhao L, Luo X, Zhou Y, Li X, Liu J, Zhan W, Liu N, Wang H, Chen G, Cai Y, Xu G, Wang W, Zheng D, Yan J (2016) Genome-wide dissection of the maize ear genetic architecture using multiple populations. New Phytol 210:1095–1106
pubmed: 26715032
doi: 10.1111/nph.13814
pmcid: 26715032
Xiao Y, Liu H, Wu L, Warburton M, Yan J (2017) Genome-wide association studies in maize: praise and stargaze. Mol Plant 10:359–374
pubmed: 28039028
doi: 10.1016/j.molp.2016.12.008
pmcid: 28039028
Xu L, Hu K, Zhang Z, Guan C, Chen S, Hua W, Li J, Wen J, Yi B, Shen J, Ma C, Tu J, Fu T (2016) Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.). DNA Res 23:43–52
pubmed: 26659471
pmcid: 26659471
Zhang HB, Li Y, Wang B, Chee PW (2008) Recent advances in cotton genomics. Int J Plant Sci 2008:742304
Zhang N, Gibon Y, Wallace JG, Lepak N, Li P, Dedow L, Chen C, So YS, Kremling K, Bradbury PJ, Brutnell T, Stitt M, Buckler ES (2015) Genome-wide association of carbon and nitrogen metabolism in the maize nested association mapping population. Plant Physiol 168:575–583
pubmed: 25918116
pmcid: 4453775
doi: 10.1104/pp.15.00025
Zhang Z, Shang H, Shi Y, Huang L, Li J, Ge Q, Gong J, Liu A, Chen T, Wang D, Wang Y, Palanga KK, Muhammad J, Li W, Lu Q, Deng X, Tan Y, Song W, Cai J, Li P, Rashid HO, Gong W, Yuan Y (2016) Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to quantitative trait loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.). BMC Plant biol 16(1):79
pubmed: 27067834
pmcid: 4827241
doi: 10.1186/s12870-016-0741-4
Zhao Y, Wang H, Chen W, Li Y, Gong H, Sang X, Huo F, Zeng F (2014) Genetic diversity and population structure of elite cotton (Gossypium hirsutum L.) germplasm revealed by SSR markers. Plant Syst Evol 301:327–336
doi: 10.1007/s00606-014-1075-z
Zhou Y, Li B, Li M, Li X, Zhang Z, Li Y, Li X (2013) A MADS-box gene is specifically expressed in fibers of cotton (Gossypium hirsutum) and influences plant growth of transgenic Arabidopsis in a GA-dependent manner. Plant Physiol Bioch 75:70–79
doi: 10.1016/j.plaphy.2013.12.003