Genomic loci associated with leaf abscission contribute to machine picking and environmental adaptability in upland cotton (Gossypium hirsutum L.),Journal of Advanced Research

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Genomic loci associated with leaf abscission contribute to machine picking and environmental adaptability in upland cotton (Gossypium hirsutum L.)
Journal of Advanced Research ( IF 10.7 ) Pub Date : 2023-05-24 , DOI: 10.1016/j.jare.2023.05.007
Hongge Li ₁ , Xiangru Wang ₂ , Ning Qin ₃ , Daowu Hu ₄ , Yinhua Jia ₁ , Gaofei Sun ₅ , Liangrong He ₆ , Hengheng Zhang ₂ , Panhong Dai ₅ , Zhen Peng ₁ , Nianchang Pang ₂ , Zhaoe Pan ₂ , Xiaomeng Zhang ₂ , Qiang Dong ₂ , Baojun Chen ₂ , Huiping Gui ₂ , Baoyin Pang ₂ , Xiling Zhang ₂ , Shoupu He ₁ , Meizhen Song ₁ , Xiongming Du ₇

Affiliation

National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China.
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; College of Agriculture, Tarim University, Alar 843300, China.
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
Anyang Institute of Technology, Anyang 455000, China.
College of Agriculture, Tarim University, Alar 843300, China.
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.

Defoliation by applying defoliants before machine picking is an important agricultural practice that enhances harvesting efficiency and leads to increased raw cotton purity. However, the fundamental characteristics of leaf abscission and the underlying genetic basis in cotton are not clearly understood. In this study, we aimed to (1) reveal the phenotypic variations in cotton leaf abscission, (2) discover the whole-genome differentiation sweeps and genetic loci related to defoliation, (3) identify and verify the functions of key candidate genes associated with defoliation, and (4) explore the relationship between haplotype frequency of loci and environmental adaptability. Four defoliation-related traits of 383 re-sequenced accessions were investigated in four environments. The genome-wide association study (GWAS), linkage disequilibrium (LD) interval genotyping and functional identification were conducted. Finally, the haplotype variation related to environmental adaptability and defoliation traits was revealed. Our findings revealed the fundamental phenotypic variations of defoliation traits in cotton. We showed that defoliant significantly increased the defoliation rate without incurring yield and fiber quality penalties. The strong correlations between defoliation traits and growth period traits were observed. A genome-wide association study of defoliation traits identified 174 significant SNPs. Two loci ( on A02 and on A13) that significantly associated with the relative defoliation rate were described, and key candidate genes and encoding a leucine-rich repeat (LRR) family protein and D3-type cell cyclin 1 protein respectively, were functional verified by expression pattern analysis and gene silencing. We found that combining of two favorable haplotypes (Hap and Hap) improved sensitivity to defoliant. The favorable haplotype frequency generally increased in high latitudes in China, enabling adaptation to the local environment. Our findings lay an important foundation for the potentially broad application of leveraging key genetic loci in breeding machine-pickable cotton.

更新日期：2023-05-24

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