Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits

Fang, Lei; Wang, Qiong; Hu, Yan; Jia, Yulin; Chen, Jiedan; Liu, Bingliang; Zhang, Zhiyuan; Guan, Xueying; Chen, Shuqi; Zhou, Baoliang; Mei, Gaofu; Sun, Jingsheng; Pan, Zhaoe; He, Shoupu; Shuhua, Xiao; Shi, Weijun; Gong, Wenfang; Liu, Jianguang; Ma, Jun; Cai, Caiping; Zhu, Xiefei; Guo, Wenshan; Du, Xinying; Zhang, Tianzhen

doi:10.1038/ng.3887

Cited by 317 publications

(354 citation statements)

References 51 publications

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“…Recent studies in rice (Caicedo et al, 2007;Li, Li, Jia, Caicedo, & Olsen, 2017), tomato (Lin et al, 2014), and maize have shown that high genetic differentiation among populations reflects adaptation to specific agroclimatic zones. Population genomic approaches for identifying signatures of selection include decreased pairwise nucleotide diversity, composite likelihood ratio (CLR) analysis for selective sweeps, and genome-environment associations (GEA) (Fang et al, 2017;Fournier-Level et al, 2011;Lasky et al, 2015;Li et al, 2017;Lin et al, 2014). The CLR analysis in SweeD is relatively robust to demographic events because the method conservatively estimates the neutral site frequency spectrum (SFS) based on the observed data (Nielsen et al, 2005;Pavlidis, Živković, Stamatakis, & Alachiotis, 2013).…”

Section: Introductionmentioning

confidence: 99%

Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal

Faye

Maina

et al. 2019

Ecology and Evolution

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Uncovering the genomic basis of climate adaptation in traditional crop varieties can provide insight into plant evolution and facilitate breeding for climate resilience. In the African cereal sorghum (Sorghum bicolor L. [Moench]), the genomic basis of adaptation to the semiarid Sahelian zone versus the subhumid Soudanian zone is largely unknown. To address this issue, we characterized a large panel of 421 georeferenced sorghum landrace accessions from Senegal and adjacent locations at 213,916 single‐nucleotide polymorphisms (SNPs) using genotyping‐by‐sequencing. Seven subpopulations distributed along the north‐south precipitation gradient were identified. Redundancy analysis found that climate variables explained up to 8% of SNP variation, with climate collinear with space explaining most of this variation (6%). Genome scans of nucleotide diversity suggest positive selection on chromosome 2, 4, 5, 7, and 10 in durra sorghums, with successive adaptation during diffusion along the Sahel. Putative selective sweeps were identified, several of which colocalize with stay‐green drought tolerance (Stg) loci, and a priori candidate genes for photoperiodic flowering and inflorescence morphology. Genome‐wide association studies of photoperiod sensitivity and panicle compactness identified 35 and 13 associations that colocalize with a priori candidate genes, respectively. Climate‐associated SNPs colocalize with Stg3a, Stg1, Stg2, and Ma6 and have allelic distribution consistent with adaptation across Sahelian and Soudanian zones. Taken together, the findings suggest an oligogenic basis of adaptation to Sahelian versus Soudanian climates, underpinned by variation in conserved floral regulatory pathways and other systems that are less understood in cereals.

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Section: Introductionmentioning

confidence: 99%

Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal

Faye

Maina

et al. 2019

Ecology and Evolution

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“…Most prior genetic diversity studies have suggested that no obvious genetic structure exists in Chinese upland cotton populations (Fang et al ; Sun et al ; Wang et al ). In our study, we present strong evidence that CUCSG has highly divergent genomic signatures for the different lineages.…”

Section: Discussionmentioning

confidence: 99%

“…However, the number of markers and genome coverage was limited, leading to uncertainty about the population structure and, thus, hampering the identification of favorable alleles. Recent single‐nucleotide polymorphism (SNP)‐based studies were also unable to clearly illuminate the population structure of upland cotton (Fang et al ; Sun et al ; Wang et al ).…”

Section: Introductionmentioning

confidence: 99%

Genomic divergence in cotton germplasm related to maturity and heterosis

Sun

Huang

et al. 2018

JIPB

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Commercial varieties of upland cotton (Gossypium hirsutum) have undergone extensive breeding for agronomic traits, such as fiber quality, disease resistance, and yield. Cotton breeding programs have widely used Chinese upland cotton source germplasm (CUCSG) with excellent agronomic traits. A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles. Here, we analyzed 10,522 high‐quality single‐nucleotide polymorphisms (SNP) with the CottonSNP63K microarray in 137 cotton accessions (including 12 hybrids of upland cotton). These data were used to investigate the genetic diversity, population structure, and genomic characteristics of each population and the contribution of these loci to heterosis. Three subgroups were identified, in agreement with their known pedigrees, geographical distributions, and times since introduction. For each group, we identified lineage‐specific genomic divergence regions, which potentially harbor key alleles that determine the characteristics of each group, such as early maturity‐related loci. Investigation of the distribution of heterozygous loci, among 12 commercial cotton hybrids, revealed a potential role for these regions in heterosis. Our study provides insight into the population structure of upland cotton germplasm. Furthermore, the overlap between lineage‐specific regions and heterozygous loci, in the high‐yield hybrids, suggests a role for these regions in cotton heterosis.

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“…In addition, re‐sequencing the genome for which there is a reference genome available permits exploration of the association between sequence variations. Recent comprehensive genome assessment by genome‐wide re‐sequencing of 34 (Page et al ., ), 318 (Fang et al ., ), 147 (Fang et al ., ) and 352 (Wang et al ., ) cotton accessions represented extensive collections in order to identify genome regions that are signature of selection. These studies provide new genomic resources that significantly advance molecular breeding in cotton.…”

Section: Cotton Genome Sequencing: Progress and Implicationsmentioning

confidence: 99%

Recent insights into cotton functional genomics: progress and future perspectives

Ashraf

Zuo

Wang

et al. 2018

Plant Biotechnology Journal

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SummaryFunctional genomics has transformed from futuristic concept to well‐established scientific discipline during the last decade. Cotton functional genomics promise to enhance the understanding of fundamental plant biology to systematically exploit genetic resources for the improvement of cotton fibre quality and yield, as well as utilization of genetic information for germplasm improvement. However, determining the cotton gene functions is a much more challenging task, which has not progressed at a rapid pace. This article presents a comprehensive overview of the recent tools and resources available with the major advances in cotton functional genomics to develop elite cotton genotypes. This effort ultimately helps to filter a subset of genes that can be used to assemble a final list of candidate genes that could be employed in future novel cotton breeding programme. We argue that next stage of cotton functional genomics requires the draft genomes refinement, re‐sequencing broad diversity panels with the development of high‐throughput functional genomics tools and integrating multidisciplinary approaches in upcoming cotton improvement programmes.

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Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits

Cited by 317 publications

References 51 publications

Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal

Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal

Genomic divergence in cotton germplasm related to maturity and heterosis

Recent insights into cotton functional genomics: progress and future perspectives

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