Abstract
Senescence in plants is a complex trait, which is controlled by both genetic and environmental factors and can affect the yield and quality of cotton. However, the genetic basis of cotton senescence remains relatively unknown. In this study, we reported genome-wide association studies (GWAS) based on 185 accessions of upland cotton and 26,999 high-quality single-nucleotide polymorphisms (SNPs) to reveal the genetic basis of cotton senescence. To determine cotton senescence, we evaluated eight traits/indices. Our results revealed a high positive correlation (r>0.5) among SPAD value 20 days after topping (SPAD20d), relative difference of SPAD (RSPAD), nodes above white flower on topping day (NAWF0d), nodes above white flower 7 days after topping (NAWF7d), and number of open bolls on the upper four branches (NB), and genetic analysis revealed that all traits had medium or high heritability ranging from 0.53 to 0.86. Based on a multi-locus method (FASTmrMLM), a total of 63 stable and significant quantitative trait nucleotides (QTNs) were detected, which represented 50 genomic regions (GWAS risk loci) associated with cotton senescence. We observed three reliable loci located on chromosomes A02 (A02_105891088_107196428), D03 (D03_37952328_38393621) and D13 (D13_59408561_60730103) because of their high repeatability. One candidate gene (Ghir_D03G011060) was found in the locus D03_37952328_38393621, and its Arabidopsis thaliana homologous gene (AT5G23040) encodes a cell growth defect factor-like protein (CDF1), which might be involved in chlorophyll synthesis and cell death. Moreover, qRT-PCR showed that the transcript level of Ghir_D03G011060 was down-regulated in old cotton leaves, and virus-induced gene silencing (VIGS) indicated that silencing of Ghir_D03G011060 resulted in leaf chlorosis and promoted leaf senescence. In addition, two candidate genes (Ghir_A02G017660 and Ghir_D13G021720) were identified in loci A02_105891088_107196428 and D13_59408561_60730103, respectively. These results provide new insights into the genetic basis of cotton senescence and will serve as an important reference for the development and implementation of strategies to prevent premature senescence in cotton breeding programs.
Highlights
Cotton (Gossypium spp.) is an important renewable natural fiber crop and an oilseed plant
One hundred and eighty-five cotton genotypes were planted in multiple environments to evaluate the range of phenotypic variation of eight senescence-related traits (SPAD0d, SPAD10d, SPAD20d, relative SPAD difference (RSPAD), NAWF0d, NAWF7d, NB, and relative difference of boll weight (RDBW))
The mean of nodes above white flower (NAWF) value on the 7th day after topping was lower than that on the topping day (5.16 and 4.06, respectively) (Figures 1E,F and Supplementary Table S2). These results showed that SPAD and NAWF were dynamic indices of cotton growth and could be used to indicate the cotton senescence
Summary
Cotton (Gossypium spp.) is an important renewable natural fiber crop and an oilseed plant. Plant senescence is the last stage of mature cell development, which aims to degrade cellular components and reuse them (Thomas et al, 2003; Jansson and Thomas, 2008) This stage is first dependent on the age and developmental progress, but is regulated by diverse environmental factors such as temperature, darkness, pathogen infection, and nutrient deficiencies (Guo and Gan, 2012). In this regard, senescence is important for plants to adapt to different environments and survive under stress (Woo et al, 2019)
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