Qadir M, Shams M. Some agronomic and physiological aspects of salt tolerance in cotton (Gossypium hirsutum L.). J Agron Crop Sci. 1997;179:101–6.
Article
Google Scholar
Greenway H, Munns R. Mechanisms of salt tolerance in nonhalophytes. Annu Rev Plant Physiol. 1980;31:149–90.
Article
CAS
Google Scholar
Ye W, Liu J. Identification technology on salt tolerance of cotton germplasm and its application. China Cotton. 1998;25(9):37–8.
Google Scholar
Tiwari RS, Picchioni GA, Steiner RL, Jones DC, Hughs SE, Zhang J. Genetic variation in salt tolerance at the seedling stage in an interspecific backcross inbred line population of cultivated tetraploid cotton. Euphytica. 2013;194:1–11.
Article
Google Scholar
Flowers TJ. Improving crop salt tolerance. J Exp Bot. 2004;55:307–19.
Article
CAS
PubMed
Google Scholar
Ashraf M, Foolad MR. Crop breeding for salt tolerance in the era of molecular markers and marker-assisted selection. Plant Breed. 2013;132:10–20.
Article
Google Scholar
Zhang D, Song HN, Chen H, Hao DR, Wang H, Kan GZ, et al. The acid phosphatase-encoding gene GmACP1 contributes to soybean tolerance to low-phosphorus stress. PLoS Genet. 2014;10(1):e1004061.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chu S, Wang J, Zhu Y, Liu S, Zhou X, Zhang H, et al. An R2R3-type MYB transcription factor, GmMYB29, regulates isoflavone biosynthesis in soybean. PLoS Genet. 2017;13(5):e1006770.
Article
PubMed
PubMed Central
CAS
Google Scholar
Iquira E, Humira S, François B. Association mapping of QTLs for sclerotinia stem rot resistance in a collection of soybean plant introductions using a genotyping by sequencing (GBS) approach. BMC Plant Biol. 2015;15:5.
Article
PubMed
PubMed Central
Google Scholar
Nambeesan SU, Mandel JR, Bowers JE, Marek L, Ebert D, Corbi J, et al. Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching. BMC Plant Biol. 2015;15:84.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zanke CD, Rodemann B, Ling J, Muqaddasi QH, Plieske J, Polley A, et al. Genome-wide association mapping of resistance to eyespot disease (Pseudocercosporella herpotrichoides) in European winter wheat (Triticum aestivum L.) and fine-mapping of Pch1. Theor Appl Genet. 2017;130:505–14.
Article
CAS
PubMed
Google Scholar
Zhao Y, Wang H, Chen W, Zhao P, Gong H, Sang X, et al. Regional association analysis-based fine mapping of three clustered QTL for verticillium wilt resistance in cotton (G. hirsutum L.). BMC Genomics. 2017;18:661.
Article
PubMed
PubMed Central
CAS
Google Scholar
Rahimi Y, Bihamta MR, Taleei A, Alipour H, Ingvarsson PK. Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs. BMC Plant Biol. 2019;19(1):541.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thapa R, Tabien RE, Thomson MJ, Septiningsih EM. Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in rice. Front Genet. 2020;11:22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edae EA, Olivera PD, Jin Y, Poland JA, Rouse MN. Genotype-by-sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata, a wild relative of cultivated wheat. BMC Genomics. 2016;17:1039.
Article
PubMed
PubMed Central
CAS
Google Scholar
Navarro J, Wilcox M, Burgueño J, Romay C, Swarts K, Trachsel S, et al. A study of allelic diversity underlying flowering-time. Nat Genet. 2017;49:476–80.
Article
CAS
Google Scholar
Wu X, Guo X, Wang A, Liu P, Wu W, Zhao Q, et al. Quantitative trait loci mapping of plant architecture-related traits using the high-throughput genotyping by sequencing method. Euphytica. 2019;215(12):212.
Article
CAS
Google Scholar
Saxena RK, Kale S, Mir RR, Mallikarjuna N, Yadav P, Das RR, et al. Genotyping-by-sequencing and multilocation evaluation of two interspecifc backcross populations identify QTLs for yield-related traits in pigeonpea. Theor Appl Genet. 2020;133(3):737–49.
Article
CAS
PubMed
Google Scholar
Peterson GW, Dong YB, Horbach C, Fu YB. Genotyping by-sequencing for plant genetic diversity analysis: a lab guide for SNP genotyping. Diversity. 2014;6:665–80.
Article
Google Scholar
Reinisch AJ, Dong JM, Brubaker CL, et al. A detailed RFLP map of cotton, Gossypium hirsutum × Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics. 1994;138:829–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jia Y, Sun J, Wang X, Zhou Z, Pan Z, He S, et al. Molecular diversity and association analysis of drought and salt tolerance in Gossypium hirsutum L. Germplasm. J Integr Agric. 2014;13(9):1845–53.
Article
CAS
Google Scholar
Du L, Cai C, Wu S, Zhang F, Hou S, Guo W. Evaluation and exploration of favorable QTL alleles for salt stress related traits in cotton cultivars (G. hirsutum L.). PLoS One. 2016;11(3):e0151076.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhao YL, Wang HM, Shao BX, Chen W, Guo ZJ, Gong HY, et al. SSR-based association mapping of salt tolerance in cotton (Gossypium hirsutum L.). Genet Mol Res. 2016;15(2):gmr.15027370.
Article
Google Scholar
Sun Z, Li H, Zhang Y, Li Z, Ke H, Wu L, et al. Identification of SNPs and candidate genes associated with salt tolerance at the seedling stage in cotton (Gossypium hirsutum L.). Front Plant Sci. 2018;9:1011.
Article
PubMed
PubMed Central
Google Scholar
Yasir M, He S, Sun G, Geng X, Pan Z, Gong W, et al. A genome-wide association study revealed key SNPs/genes associated with salinity stress tolerance in upland cotton. Genes. 2019;10:829.
Article
PubMed Central
CAS
Google Scholar
Stich B, Maurer HP, Melchinger AE, Frisch M, Heckenberger M, van der Voort JR, et al. Comparison of linkage disequilibrium in elite European maize inbred lines using AFLP and SSR markers. Mol Breed. 2006;17:217–26.
Article
CAS
Google Scholar
Yang XH, Yan JB, Zheng YP, Yu JM, Li JS. Reviews of association analysis for quantitative traits in plants. Acta Agron Sin. 2007;33:523–30.
CAS
Google Scholar
Sun Z, Wang X, Liu Z, Gu Q, Zhang Y, Li Z, et al. Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L. Plant Biotechnol J. 2017;15(8):982–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang C, Nie X, Shen C, You C, Li W, Zhao W, et al. 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. 2017;15:1374–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hu Y, Chen J, Fang L, Zhang Z, Ma W, Niu Y, et al. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. Nat Genet. 2019;51(4):739–48.
Article
CAS
PubMed
Google Scholar
Xu P, Yang Y, Guo Q, Zhang X, Xu Z, Shen X. Development of EST-SSR and EST-InDel markers associated with salt tolerance in upland cotton. Cotton Sci. 2016;28(1):65–74.
Google Scholar
Zhao J, Gao Y, Zhang Z, Chen T, Guo W, Zhang T. A receptor-like kinase gene (GbRLK) from Gossypium barbadense enhances salinity and drought-stress tolerance in Arabidopsis. BMC Plant Biol. 2013;13:110.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chang W, Liu X, Zhu J, Fan W, Zhang Z. An aquaporin gene from halophyte Sesuvium portulacastrum, SpAQP1, increases salt tolerance in transgenic tobacco. Plant Cell Rep. 2016;35:385–95.
Article
CAS
PubMed
Google Scholar
Flint-Garcia SA, Thuillet AC, Yu JM, Pressoir G, Romero SM, Mitchell SE, et al. Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J. 2005;44:1054–64.
Article
CAS
PubMed
Google Scholar
Nie X, Huang C, You C, Li W, Zhao W, Shen C, et al. Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China. BMC Genomics. 2016;17:352.
Article
PubMed
PubMed Central
CAS
Google Scholar
Fang L, Wang Q, Hu Y, Jia Y, Chen J, Liu B, et al. Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits. Nat Genet. 2017;49:1089–98.
Article
CAS
PubMed
Google Scholar
Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, et al. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet. 2017;49:579–87.
Article
CAS
PubMed
Google Scholar
Dong C, Wang J, Chen Q, Yu Y, Li B. Detection of favorable alleles for yield and yield components by association mapping in upland cotton. Genes Genomics. 2018;40:725–34.
Article
PubMed
Google Scholar
Ma J, Liu J, Pei W, Ma Q, Wang N, Zhang X, et al. Genome-wide association study of the oil content in upland cotton (Gossypium hirsutum L.) and identification of GhPRXR1, a candidate gene for a stable QTL qOC-Dt5-1. Plant Sci. 2019;286:89–97.
Article
CAS
PubMed
Google Scholar
Zhu G, Gao W, Song X, Sun F, Hou S, Liu N, et al. Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.). BMC Plant Biol. 2020;20(1):23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo WZ, Zhang TZ, Zhu XF, Pan JJ. Modified backcross pyramiding breeding with molecular marker-assisted selection and its applications in cotton. Acta Agron Sin. 2005;31(8):963–70.
CAS
Google Scholar
Kapilan R, Vaziri M, Zwiazek JJ. Regulation of aquaporins in plants under stress. Biol Res. 2018;51:4.
Article
PubMed
PubMed Central
CAS
Google Scholar
Xu Y, Hu W, Liu J, Song S, Hou X, Jia C, et al. An aquaporin gene MaPIP2-7 is involved in tolerance to drought, cold and salt stresses in transgenic banana (Musa acuminate L.). Plant Physiol Biochem. 2020;147:66–76.
Article
CAS
PubMed
Google Scholar
Wang X, Li Y, Ji W, Bai X, Cai H, Zhu D, et al. A novel Glycine soja tonoplast intrinsic protein gene responds to abiotic stress and depresses salt and dehydration tolerance in transgenic Arabidopsis thaliana. J Plant Physiol. 2011;168:1241–8.
Article
CAS
PubMed
Google Scholar
Jiang JY, Lee SH, Rhee JY, Chung GC, Ahn SJ, Kang H. Transgenic Arabidopsis and tobacco plants overexpressing an aquaporin respond differently to various abiotic stresses. Plant Mol Biol. 2007;64:621–32.
Article
CAS
Google Scholar
He X, Tian J, Yang L, Huang Y, Zhao B, Zhou C, et al. Overexpressing a glycogen synthase kinase gene from wheat, TaGSK1, enhances salt tolerance in transgenic Arabidopsis. Plant Mol Biol Report. 2012;30(4):807.
Article
CAS
Google Scholar
Paterson AH, Brubaker CL, Wendel JF. A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Mol Biol Report. 1993;11(2):122–7.
Article
CAS
Google Scholar
Fan L, Wang L, Wang X, Zhang H, Zhu Y, Guo J, et al. A high-density genetic map of extra-long staple cotton (Gossypium barbadense) constructed using genotyping-by sequencing based single nucleotide polymorphic markers and identification of fiber traits-related QTL in a recombinant inbred line population. BMC Genomics. 2018;19:489.
Article
PubMed
PubMed Central
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25(14):1754–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945–59.
Article
CAS
PubMed
PubMed Central
Google Scholar
Evanno G, Regaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005;14:2611–20.
Article
CAS
PubMed
Google Scholar
Hardy OJ, Vekemans X. SPAGEDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes. 2002;2:618–20.
Article
CAS
Google Scholar
Bradbury PJ, Zhang Z, Kroon DE, Casstevens RM, Ramdoss Y, Buckler ES. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007;23:2633–5.
Article
CAS
PubMed
Google Scholar
Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet. 2006;38:203–8.
Article
CAS
PubMed
Google Scholar
Hu G, Yu S. Extraction of high-quality total RNA in cotton leaf with improved CTAB method. Cotton Sci. 2007;19:69–70.
Google Scholar
Xu P, Gao J, Cao Z, Chee PW, Guo Q, Xu Z, et al. Fine mapping and candidate gene analysis of qFL-chr1, a fiber length QTL in cotton. Theor Appl Genet. 2017;130:1309–19.
Article
CAS
PubMed
Google Scholar
Gao X, Britt RC Jr, Shan L, He P. Agrobacterium mediated virus-induced gene silencing assay in cotton. J Vis Exp. 2011;54:e2938.
Google Scholar