Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton

Abstract

Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton. A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block. Furthermore, 21 candidate genes for plant architecture were predicted in a 0.95-Mb region including the four peak SNPs. One of these genes (Gh_D03G0922) was near the significant SNP D03_31584163 (8.40 kb), and its Arabidopsis homologs contain MADS-box domains that might be involved in plant growth and development. qRT-PCR showed that the expression of Gh_D03G0922 was upregulated in the apical buds and young leaves of the short and compact cotton varieties, and virus-induced gene silencing (VIGS) proved that the silenced plants exhibited increased PH. These results indicate that Gh_D03G0922 is likely the candidate gene for PH in cotton. The genetic variations and candidate genes identified in this study lay a foundation for cultivating moderately short and compact varieties in future Chinese cotton-breeding programs.

QTL mapping for plant height and fruit branch number based on RIL population of upland cotton

“…In the current study, QTL mapping for agronomic traits is based on a high-density genetic map that covers a total genetic distance of 2 477.99 cM, composing 4 729 SNP markers and 122 SSR markers. Comparing the results of this study with previous common QTLs summarized with meta-analysis (Said et al 2013), and QTLs identified in recent years (Jia et al 2016;Su et al 2018;Zhang et al 2019a;Zhang et al 2019b;Ma et al 2019a), QTLs on c04 for PH and those on c01, c07, c12, c20-c21, c24, and c26 for FBN were all newly identified ones. As the existence of significant G × E interactions, QTLs identified in every environment moved around.…”

“…However, in current studies, when SNPs were applied to map the QTL, although it was not easy to compare common markers, it was convenient to identify the physical position of the QTL. In recent studies (Su et al 2018;Zhang et al 2019a), the physical positions of stable QTLs for PH and FBN traits were clearly shown. When comparing these studies with our current study, the QTLs of qPH-c17-1 and qPH-c19-1 were probably previously identified by Zhang et al (2019a) and Su et al (2018), respectively.…”

“…PH is an important component of ideal plant architecture and plays an important role in cotton breeding (Jiao et al 2010;Ma et al 2019b;Miura et al 2010;Wang et al 2018). Studies demonstrated that PH and FBN had important effects on cotton yield and mechanical harvesting (Su et al 2018;Ma et al 2019b), but it is still necessary for researchers to understand the genetic basis of PH and FBN and how they impact plant architecture (Qi et al 2017;Shang et al 2016;Song and Zhang 2009;Wang et al 2006;Zhang et al 2006). Therefore, further study on these agronomic traits will be of great significance for cotton plant-type breeding and the application and distribution of mechanical harvesting technologies in cotton production.…”

“…Due to the rapid development of highthroughput sequencing technologies, the reduction of sequencing cost, and the establishment of the reference genome of upland cotton (TM-1), a number of highdensity genetic maps have been constructed by single nucleotide polymorphism (SNP) markers including genotyping by sequencing (GBS) (Diouf et al 2018;Qi et al 2017), restriction-site associated DNA sequencing (RAD-Seq) (Hegarty et al 2013;Kundu et al 2015;Wang et al 2017), specific locus-amplified fragment sequencing (SLAF-seq) (Ali et al 2018;Zhang et al 2016), CottonSNP63K array (Hulse-Kemp et al 2015;Li et al 2016;Li et al 2018a;Zhang et al 2016), and Cot-tonSNP80K array (Cai et al 2017;Tan et al 2018;Liu et al 2018;Zou et al 2018). These high-density genetic maps significantly improved QTL detection accuracy (Ma et al 2019a;Su et al 2018;Jia et al 2016).…”

Role of SNPs in determining QTLs for major traits in cotton

“…In another study, 93 250 SNPs for five plant architecture traits were found in 355 Chinese upland cotton accessions using the SLAF-Seq method. GWAS revealed 22 highly associated SNPs and 21 candidate genes for these traits (Su et al 2018). Molecular analysis of the short fruiting branch gene was carried out in an F 2 population between two parents, one with short fruiting branches and the other with long fruiting branches.…”