Dissection of the genetic variation and candidate genes of lint percentage by a genome-wide association study in upland cotton

Song, Chengxiang; Li, Wei; Pei, Xinwu; Liu, Yangai; Ren, Zhongying; He, Kunlun; Zhang, Fei; Sun, Kuan; Zhou, Xin; Ma, Xiongfeng; Yang, Daigang

doi:10.1007/s00122-019-03333-0

Cited by 42 publications

(65 citation statements)

References 65 publications

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“…It is notable that, congruent with other QTL analyses, we find important fiber related QTL on the subgenome derived from the parent with the much shorter, inferior fiber (D genome). The involvement of the D-genome in the evolution of transgressive fiber phenotypes has been noted in multiple analyses, including for QTL (Jiang et al 1998;Lacape et al 2005;Han et al 2006;Rong et al 2007;Qin et al 2008;Said et al 2015b), expression (Hovav et al 2008a;Yoo and Wendel 2014;Zhang et al 2015;Fang et al 2017b), and in selective genomic sweeps (Fang et al 2017a(Fang et al , 2017cSong et al 2019), yet the underlying genetic basis for this phenomenon remains unclear. Further work using advanced populations in which individual QTL have been isolated in isogenic backgrounds, combined with a multi-omics or systems biology perspective, is one promising approach for developing a fuller understanding of cotton biology as well as the domestication process.…”

Section: Discussionmentioning

confidence: 99%

Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutumL.)

Grover

Yoo

Meng

et al. 2020

G3 Genes|Genomes|Genetics

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The evolution and domestication of cotton is of great interest from both economic and evolutionary standpoints. Although many genetic and genomic resources have been generated for cotton, the genetic underpinnings of the transition from wild to domesticated cotton remain poorly known. Here we generated an intraspecific QTL mapping population specifically targeting domesticated cotton phenotypes. We used 466 F2 individuals derived from an intraspecific cross between the wild Gossypium hirsutum var. yucatanense (TX2094) and the elite cultivar G. hirsutum cv. Acala Maxxa, in two environments, to identify 120 QTL associated with phenotypic changes under domestication. While the number of QTL recovered in each subpopulation was similar, only 22 QTL were considered coincident (i.e., shared) between the two locations, eight of which shared peak markers. Although approximately half of QTL were located in the A-subgenome, many key fiber QTL were detected in the D-subgenome, which was derived from a species with unspinnable fiber. We found that many QTL are environment-specific, with few shared between the two environments, indicating that QTL associated with G. hirsutum domestication are genomically clustered but environmentally labile. Possible candidate genes were recovered and are discussed in the context of the phenotype. We conclude that the evolutionary forces that shape intraspecific divergence and domestication in cotton are complex, and that phenotypic transformations likely involved multiple interacting and environmentally responsive factors.

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Section: Discussionmentioning

confidence: 99%

Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutumL.)

Grover

Yoo

Meng

et al. 2020

G3 Genes|Genomes|Genetics

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“…Many candidate genes that underlie traits such as cotton fiber yield and quality [11][12][13][14], and seed oil composition and protein content [15], have been revealed. In addition, several studies on stress tolerance have been carried out in cotton.…”

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confidence: 99%

Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.)

Zhu

Gao

Song

et al. 2019

Preprint

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Background: Salinity is one of the most significant environmental factors limiting the productivity of cotton. However, the key genetic components responsible for the reduction in cotton yield in saline-alkali soils are still unclear. Results: Here, we evaluated three main components of lint yield, single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP), across 316 G. hirsutum accessions under four salt conditions over two years. Phenotypic analysis indicated that LP was unchanged under different salt conditions, however BNPP decreased significantly and SBW increased slightly under high salt conditions. Based on 57,413 high-quality single nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) analysis, a total of 42, 91 and 25 stable quantitative trait loci (QTLs) were identified for SBW, LP and BNPP, respectively. Phenotypic and QTL analysis suggested that there was little correlation among the three traits. For LP, 8 stable QTLs were detected simultaneously in four different salt conditions, while fewer repeated QTLs for SBW or BNPP were identified. Gene Ontology (GO) analysis indicated that their regulatory mechanisms were also quite different. Via transcriptome profile data, we detected that 10 genes from the 8 stable LP QTLs were predominantly expressed during fiber development. Further, haplotype analyses found that a MYB gene (GhMYB103), with the two SNP variations in cis-regulatory and coding regions, was significantly correlated with lint percentage, implying a crucial role in lint yield. We also identified that 40 candidate genes from BNPP QTLs were salt-inducible. Genes related to carbohydrate metabolism and cell structure maintenance were rich in plants grown in high salt conditions, while genes related to ion transport were active in plants grown in low salt conditions, implying different regulatory mechanisms for BNPP at high and low salt conditions. Conclusions: This study provides a foundation for elucidating cotton salt tolerance mechanisms and contributes gene resources for developing Upland cotton varieties with high yields and salt stress tolerance.

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“…In total, 854 QTNs on 26 chromosomes were identified as significantly associated with the three traits (Additional file 8: Table S6). Following the linkage disequilibrium (LD) value [17] and referring the method reported by Song et al (2019) [19], the 200-kb upstream and downstream of QTNs were defined as one QTL. In total, 600 QTLs including 151 of SBW, 417 of LP and 112 of BNPP, were detected with 1446 times under different environments and BLUPs by six multi-loci MLM models (Table 1).…”

Section: Gwas Of the Lint Yield Related Traitsmentioning

confidence: 99%

“…Following the LD value [17] and referring the method reported by Song et al (2019) [19], the 200 kb upstream and downstream of QTNs were defined as QTLs. The distance of two QTNs less than 200 kb will be merged into a single QTL.…”

Section: Qtls and Candidate Genes Identificationmentioning

confidence: 99%

Genome-wide association study reveals genetic variation and candidate genes of lint yield components under salt field conditions in cotton (Gossypium hirsutum L.)

Zhu¹,

Gao²,

Song³

et al. 2019

Preprint

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Background Salinity is one of the most decisive environmental factors limiting the productivity of cotton. However, the key genetic components leading to the reduction of cotton yield in saline-alkali soils are still unclear. Results Here, we evaluated three main components of lint yield across 316 G. hirsutum accessions, including single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP), under four salt conditions for two years. Phenotypic analysis indicated that LP showed no change under different salt conditions, however BNPP decreased significantly while SBW increased slightly under high salt condition. Based on 57,413 high-quality single nucleotide polymorphisms (SNPs) and genome-wide association studies (GWAS) analysis, a total of 42, 91 and 25 stable quantitative trait loci (QTLs) were identified for SBW, LP and BNPP, respectively. Few overlapped QTLs and no significant phenotypic correlation among the three traits was observed. Gene Ontology (GO) analysis indicated that their regulatory mechanisms were also quite different. There were 8 overlapped QTLs for LP while fewer for SBW and BNPP identified by comparing different salt conditions. We detected that 10 genes from the 8 stable LP QTLs were predominantly expressed during fiber development. Further, haplotype analyses found that a MYB gene ( GhMYB103 ) with the two SNP variations in cis-regulatory and coding regions, was significantly correlated with lint percentage, implying the crucial role in lint yield. With transcriptome analysis, we identified that 40 candidate genes from BNPP QTLs were salt-inducible. However, these genes exhibited different regulation pattern. Genes related to carbohydrate metabolism and cell structure maintenance were rich in high salt condition, while genes related to ion transport were active in low salt condition. Conclusions This study provides a foundation for elucidating cotton salt tolerance mechanism and contributes gene resources for developing varieties with high yield and salt stress tolerance in upland cotton.

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Dissection of the genetic variation and candidate genes of lint percentage by a genome-wide association study in upland cotton

Cited by 42 publications

References 65 publications

Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutumL.)

Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutumL.)

Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.)

Genome-wide association study reveals genetic variation and candidate genes of lint yield components under salt field conditions in cotton (Gossypium hirsutum L.)

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