与叶片脱落相关的基因组位点有助于陆地棉（Gossypium hirsutum L.）的机械采摘和环境适应性。

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

机构信息

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.

出版信息

J Adv Res. 2024 Apr;58:31-43. doi: 10.1016/j.jare.2023.05.007. Epub 2023 May 24.

DOI:10.1016/j.jare.2023.05.007

PMID:37236544

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10982856/

Abstract

INTRODUCTION

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.

OBJECTIVES

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.

METHODS

Four defoliation-related traits of 383 re-sequenced Gossypium hirsutum 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.

RESULTS

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 (RDR7 on A02 and RDR13 on A13) that significantly associated with the relative defoliation rate were described, and key candidate genes GhLRR and GhCYCD3;1, 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.

CONCLUSION

Our findings lay an important foundation for the potentially broad application of leveraging key genetic loci in breeding machine-pickable cotton.

摘要

简介

在机械采摘前使用脱叶剂进行脱叶是提高收获效率和增加原棉纯度的重要农业措施。然而，棉花叶片脱落的基本特征和潜在的遗传基础尚不清楚。

目的

本研究旨在：（1）揭示棉花叶片脱落的表型变异；（2）发现与脱叶相关的全基因组分化扫描和遗传位点；（3）鉴定和验证与脱叶相关的关键候选基因的功能；（4）探讨位点的单倍型频率与环境适应性之间的关系。

方法

在四个环境中调查了 383 个重测序陆地棉资源的四个脱叶相关性状。进行了全基因组关联研究（GWAS）、连锁不平衡（LD）区间基因型分析和功能鉴定。最后，揭示了与环境适应性和脱叶性状相关的单倍型变异。

结果

本研究揭示了棉花脱叶性状的基本表型变异。结果表明，脱叶剂的使用可显著提高脱叶率，而不会降低产量和纤维质量。观察到脱叶性状与生长周期性状之间存在强烈的相关性。对脱叶性状的全基因组关联研究鉴定出 174 个显著 SNP。描述了与相对脱叶率显著相关的两个位点（A02 上的 RDR7 和 A13 上的 RDR13）和关键候选基因 GhLRR 和 GhCYCD3;1，分别编码富含亮氨酸重复（LRR）家族蛋白和 D3 型细胞周期蛋白 1 蛋白，通过表达模式分析和基因沉默功能验证。发现两种有利单倍型（Hap 和 Hap）的组合提高了对脱叶剂的敏感性。有利单倍型的频率在中国高纬度地区普遍增加，使其适应当地环境。