Abstract
(1) Background: Upland cotton (Gossypium hirsutum L.) is the most important natural fiber worldwide, and it is extensively planted and plentifully used in the textile industry. Major cotton planting regions are frequently affected by abiotic stress, especially drought stress. Drought resistance is a complex, quantitative trait. A genome-wide association study (GWAS) constitutes an efficient method for dissecting the genetic architecture of complex traits. In this study, the drought resistance of a population of 316 upland cotton accessions was studied via GWAS. (2) Methods: GWAS methodology was employed to identify relationships between molecular markers or candidate genes and phenotypes of interest. (3) Results: A total of 8, 3, and 6 SNPs were associated with the euphylla wilting score (EWS), cotyledon wilting score (CWS), and leaf temperature (LT), respectively, based on a general linear model and a factored spectrally transformed linear mixed model. For these traits, 7 QTLs were found, of which 2 each were located on chromosomes A05, A11, and D03, and of which 1 was located on chromosome A01. Importantly, in the candidate regions WRKY70, GhCIPK6, SnRK2.6, and NET1A, which are involved in the response to abscisic acid (ABA), the mitogen-activated protein kinase (MAPK) signaling pathway and the calcium transduction pathway were identified in upland cotton at the seedling stage under drought stress according to annotation information and linkage disequilibrium (LD) block analysis. Moreover, RNA sequencing analysis showed that WRKY70, GhCIPK6, SnRK2.6, and NET1A were induced by drought stress, and the expression of these genes was significantly different between normal and drought stress conditions. (4) Conclusions: The present study should provide some genomic resources for drought resistance in upland cotton. Moreover, the germplasm of the different phenotypes, the detected SNPs and, the potential candidate genes will be helpful for molecular marker-assisted breeding studies about increased drought resistance in upland cotton.
Highlights
Water shortages are among the most serious limitations to global agricultural production due to the complexity of water-deficient environments and climatic variation [1,2]
In order to systematically explore the genetic basis and mechanism of drought resistance traits of upland cotton, a set of 316 accessions was selected from a natural population of 355 cultivars or lines (Figure 1a,b), and the leaf temperature (LT), cotyledon wilting score (CWS), euphylla wilting score (EWS), and leaf chlorophyll content (LC), which are target traits of these accessions related to drought resistance, were evaluated and analyzed under two different greenhouse environments
Based on the pair-wise genetic distance determined using whole genome single-nucleotide polymorphism (SNP) markers among the 316 accessions, we explored the phylogenetic relationships of these cotton germplasms, which could be divided into three divergent groups (Figure 2a)
Summary
Water shortages are among the most serious limitations to global agricultural production due to the complexity of water-deficient environments and climatic variation [1,2]. Drought limits cotton (Gossypium hirsutum L.) productivity and fiber quality, drought resistance is a complex, quantitative trait controlled by more than two genes [3,4]. It is, of great significance to improve the drought tolerance of cotton and increase its yield under drought stress conditions. Allotetraploid upland cotton (Gossypium hirsutum L.; AADD, 2n = 4× = 52) is one of the most important economic crop species It produces the most significant natural fiber worldwide, is a source of seed oil, and it accounts for approximately 95% of cotton production worldwide [5]. It is a great challenge and formidable task for researchers to determine suitable drought resistance cultivation techniques and cultivate drought-tolerant cotton varieties
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