Ademe MS, He SP, Pan ZE, et al. Association mapping analysis of fiber yield and quality traits in Upland cotton (Gossypium hirsutum L.). Mol Genet Genomics. 2017; 292: 1267-1280. doi: 10.1007/s00438-017-1346-9.
An CF, Jenkins JN, Wu JX, et al. Use of fiber and fuzz mutants to detect QTL for yield components, seed, and fiber traits of upland cotton.2010; Euphytica. 172, 21-34. https://doi.org/10.1007/s10681-009-0009-2
Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing. Journal of the royal statistical society. 1995; 57, 289-300.
Bradbury PJ, Zhang Z, Kroon DE, et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics.2007; 23, 2633-2635. doi: 10.1093/bioinformatics/btm308.
Cardon GH, Höhmann S, Nettesheim K, et al. Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition. Plant J. 1997; 12, 367-377. doi: 10.1046/j.1365-313x.1997.12020367.x
Chen ZJ, Scheffler BE, Dennis E, et al. Toward sequencing cotton (Gossypium) genomes. Plant Physiol. 2007; 145, 1303-1310. doi: 10.1104/pp.107.107672.
Dong CG, Wang J, Chen QJ, et al. Detection of favorable alleles for yield and yield components by association mapping in upland cotton. Genes Genomics. 2018; 40, 725-734. doi: 10.1007/s13258-018-0678-0.
Du XM, Huang G, He SP, et al. Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nat Genet. 2018; 50, 796-802. doi: 10.1038/s41588-018-0116-x.
Fang L, Gong H, Hu Y, et al. Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons. Genome biology. 2017a; 18, 33-33. doi: 10.1186/s13059-017-1167-5.
Fang L, Wang Q, Hu Y, et al. Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits. Nat Genet. 2017b; 49, 1089-1098. doi: 10.1038/ng.3887.
Flint-Garcia SA, Thornsberry JM, Buckler ESt. Structure of linkage disequilibrium in plants. Annu Rev Plant Biol. 2003; 54, 357-374. doi: 10.1146/annurev.arplant.54.031902.134907.
Gore MA, Fang DD, Poland J, et al. Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton. The Plant Genome. 2014; 7(1):1-10. doi: 10.3835/plantgenome2013.07.0023
Gou MY, Yang XM, Zhao YJ, et al. Cytochrome b5 is an obligate electron shuttle protein for syringyl lignin biosynthesis in Arabidopsis. Plant Cell. 2019; 31, 1344-1366. doi: 10.1105/tpc.18.00778.
Hou H, Yan X, Sha T, et al. The SBP-Box Gene VpSBP11 from Chinese Wild Vitis Is Involved in Floral Transition and Affects Leaf Development. Int J Mol Sci.2017; 18(7):1493. doi: 10.3390/ijms18071493.
Huang C, Shen C, Wen TW,et al. SSR-based association mapping of fiber quality in upland cotton using an eight-way MAGIC population. Mol Genet Genomics.2018; 293, 793-805. doi: 10.1007/s00438-018-1419-4.
Huang XH, Yang SH, Gong JY, et al. 2016. Genomic architecture of heterosis for yield traits in rice. Nature.2016; 537, 629-633. doi: 10.1038/nature19760.
Hufford MB, Xu X, van Heerwaarden J, et al. Comparative population genomics of maize domestication and improvement. Nat Genet.2012; 44, 808-811. doi: 10.1038/ng.2309.
Jakobsson M, Rosenberg NA. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 2007; 23, 1801-1806. doi: 10.1093/bioinformatics/btm233.
Jia YH, Sun XW, Sun JL,et al. 2014. Association mapping for epistasis and environmental interaction of yield traits in 323 cotton cultivars under 9 different environments. PLoS One.2014; 9, e95882. doi: 10.1371/journal.pone.0095882.
Jiang C, Wright RJ, El-Zik KM,et al. Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc Natl Acad Sci U S A.1998; 95, 4419-4424. doi: 10.1073/pnas.95.8.4419.
Kaur S, Zhang X, Mohan A, et al. Genome-Wide Association Study Reveals Novel Genes Associated with Culm Cellulose Content in Bread Wheat (Triticum aestivum, L.). Front Plant Sci. 2017; 8, 1913. doi: 10.3389/fpls.2017.01913.
Li C, Zhao TL, Yu HR, et al. Genetic basis of heterosis for yield and yield components explored by QTL mapping across four genetic populations in upland cotton. BMC Genomics. 2018a; 19, 910. doi: 10.1186/s12864-018-5289-2.
Li Fj, Wen We, He Zh, et al. Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers. Theor Appl Genet. 2018b; 131, 1903-1924. doi: 10.1007/s00122-018-3122-6.
Li H, Peng ZY, Yang XH, et al. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet. 2013; 45, 43-50. doi: 10.1038/ng.2484.
Li TG, Ma XF, Li NY, et al. Genome-wide association study discovered candidate genes of Verticillium wilt resistance in upland cotton (Gossypium hirsutum L.). Plant Biotechnol J. 2017; 15, 1520-1532. doi: 10.1111/pbi.12734.
Liu RZ, Wang BH, Guo WZ, et al. Quantitative trait loci mapping for yield and its components by using two immortalized populations of a heterotic hybrid in Gossypium hirsutum L. Molecular Breeding. 2012; 29, 297-311. https://doi.org/10.1007/s11032-011-9547-0
Liu YY, You SJ, Taylor-Teeples M, et al. BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 interact and regulate secondary cell wall formation via repression of REVOLUTA. Plant Cell. 2014; 26, 4843-4861. doi: 10.1105/tpc.114.128322.
Lu XK, Fu XQ, Wang DL, et al. Resequencing of cv CRI-12 family reveals haplotype block inheritance and recombination of agronomically important genes in artificial selection. Plant Biotechnol J.2019; 17, 945-955. doi: 10.1111/pbi.13030.
Luikart G, England PR, Tallmon DA,et al. The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics. 2003; 4, 981-994. doi: 10.1038/nrg1226.
Ma XF, Wang ZY Li W, et al. Resequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement. Plant Biotechnol J. 2019; 17, 762-775. doi: 10.1111/pbi.13013.
Maik W, Abid MA, Cheema HM, et al. FROM Qutn TO Bt COTTON: DEVELOPMENT, ADOPTION AND PROSPECTS. A REVIEW. Tsitol Genet.2015; 49, 73-85.
Mei HX, Zhu XF, Zhang TZ. Favorable QTL Alleles for Yield and Its Components Identified by Association Mapping in Chinese Upland Cotton Cultivars. PLoS One.2013; 8(12):e82193. doi: 10.1371/journal.pone.0082193.
Mengistu DK, Kidane YG, Catellani M, et al. High-density molecular characterization and association mapping in Ethiopian durum wheat landraces reveals high diversity and potential for wheat breeding. Plant Biotechnol J. 2016; 14, 1800-1812. doi: 10.1111/pbi.12538.
Nachman MW, Payseur BA. Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice. Philos Trans R Soc Lond B Biol Sci. 2012; 367, 409-421. doi: 10.1098/rstb.2011.0249.
Nie XH, Huang C, You CY, 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. doi: 10.1186/s12864-016-2662-x.
Nie XH, Wen TW, Shao PX, et al. High-density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China. Plant J.2020; 103, 677-689. doi: 10.1111/tpj.14760.
Noor MA, Bennett SM. Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species. Heredity (Edinb). 2009; 103, 439-444. doi: 10.1038/hdy.2009.151.
Raihan MS, Liu J, Huang J, et al. Multi-environment QTL analysis of grain morphology traits and fine mapping of a kernel-width QTL in Zheng58 × SK maize population. Theor Appl Genet.2016; 129, 1465-1477. doi: 10.1007/s00122-016-2717-z.
Soltis NE, Atwell S, Shi G, et al. Interactions of Tomato and Botrytis cinerea Genetic Diversity: Parsing the Contributions of Host Differentiation, Domestication, and Pathogen Variation. Plant Cell. 2019; 31, 502-519. doi: 10.1105/tpc.18.00857.
Sun ZW, Wang XF, Liu ZW, et al. A genome-wide association study uncovers novel genomic regions and candidate genes of yield-related traits in upland cotton. Theor Appl Genet. 2018; 131, 2413-2425. doi: 10.1007/s00122-018-3162-y.
Wang BH, Guo WZ, Zhu XF, et al. QTL mapping of yield and yield components for elite hybrid derived-RILs in upland cotton. J Genet Genomics. 2007; 34(1):35-45. doi: 016/S1673-8527(07)60005-8.
Wang HT, Huang C, Guo HL, et al. QTL Mapping for Fiber and Yield Traits in Upland Cotton under Multiple Environments. PLoS One. 2015; 10(6):e0130742. doi: 10.1371/journal.pone.0130742.
Wang MJ, Tu LL, Yuan DJ, et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nat Genet. 2019, 51, 224-229. doi: 10.1038/s41588-018-0282-x.
Xue S, Bradbury PJ, Casstevens TM, et al. Genetic Architecture of Domestication-Related Traits in Maize. Genetics. 2016; 204, 99-113. doi: 10.1534/genetics.116.191106.
Yamasaki K, Kigawa T, Inoue M, et al. An Arabidopsis SBP-domain fragment with a disrupted C-terminal zinc-binding site retains its tertiary structure. FEBS Lett. 2006; 580, 2109-2116. doi: 10.1016/j.febslet.2006.03.014.
Yang N, Lu YL, Yang XH,et al. Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel. PLoS Genet. 2014; 10(9):e1004573. doi: 10.1371/journal.pgen.1004573.
Yuan DJ, Tang ZH, Wang MJ, et al. The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres. Sci Rep. 2015; 5, 17662. doi: 10.1038/srep17662.
Zhang D, Zhang HY, Hu ZB, et al. Artificial selection on GmOLEO1 contributes to the increase in seed oil during soybean domestication. PLoS Genet. 2019; 15(7):e1008267. doi: 10.1371/journal.pgen.1008267.
Zhang TZ, Hu Y, Jiang WK, et al. Sequencing of allotetraploid cotton ( Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol, 2015; 33, 531-537. doi: 10.1038/nbt.3207.
Zhang Z, Li JW, Jamshed M, et al. Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population. Plant Biotechnol J. 2020; 18, 239-253. doi: 10.1111/pbi.13191.
Zhao GW, Lian Q, Zhang ZH, et al. A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits. Nat Genet. 2019; 51, 1607-1615. doi: 10.1038/s41588-019-0522-8.
Zheng J, Wu H, Zhu HB, et al. Determining factors, regulation system, and domestication of anthocyanin biosynthesis in rice leaves. New Phytol. 2019; 223, 705-721. doi: 10.1111/nph.15807.
Zhou ZK, Jiang Y, Wang Z, et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol. 2015; 34, 441-441. doi: 10.1038/nbt.3096.