基因组和单倍型为研究海岛棉的种群分化和品种改良提供了见解。

Genome and haplotype provide insights into the population differentiation and breeding improvement of Gossypium barbadense.

机构信息

National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.

Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.

出版信息

J Adv Res. 2023 Dec;54:15-27. doi: 10.1016/j.jare.2023.02.002. Epub 2023 Feb 10.

DOI:10.1016/j.jare.2023.02.002

PMID:36775017

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10703724/

Abstract

INTRODUCTION

Sea-island cotton (Gossypium barbadense, Gb) is one of the major sources of high-grade natural fiber. Besides the common annual Gb cotton, perennial Gb cotton is also cultivated, but studies on perennial Gb cotton are rare.

OBJECTIVES

We aimed to make a systematic analysis of perennial sea-island cotton and lay a foundation for its utilization in breeding, and try to identify the representative structural variations (SVs) in sea-island cotton, and to reveal the population differentiation and adaptive improvement of sea-island cotton.

METHODS

Through genome assembly of one perennial Gb cotton accession (named Gb_M210936) and comparative genome analysis, variations during Gb cotton domestication were identified by comparing Gb_M210936 with annual Gb accession 3-79 and with wild allotetraploid cotton G. darwinii. Six perennial Gb accessions combining with the resequenced 1,129 cotton accessions were used to conduct population and genetic analysis. Large haplotype blocks (haploblocks), generated from interspecific introgressions and intraspecific inversions, were identified and were used to analyze their effects on population differentiation and agronomic traits of sea-island cotton.

RESULTS

One reference genome of perennial sea-island cotton was assembled. Representative SVs in sea-island cotton were identified, and 31 SVs were found to be associated with agronomic traits. Perennial Gb cotton had a closer kinship with the wild-to-landrace continuum Gb cotton from south America where Gb cotton is originally domesticated. Haploblocks were associated with agronomic traits improvement of sea-island cotton, promoted sea-island cotton differentiation into three subgroups, were suffered from breeding selection, and may drive Gb cotton to be adapted to central Asian.

CONCLUSION

Our study made up the lack of perennial Gb cotton genome, and clarified that exotic introgressions improved the traits of sea-island cotton, promoted the population differentiation, and drove sea-island cotton adaptive to central Asia, which will provide new insights for the genetic breeding improvement of sea-island cottons.

摘要

简介

海岛棉（Gossypium barbadense，Gb）是优质天然纤维的主要来源之一。除了常见的一年生 Gb 棉花外，还种植了多年生 Gb 棉花，但对多年生 Gb 棉花的研究较少。

目的

本研究旨在对多年生海岛棉进行系统分析，为其在育种中的利用奠定基础，尝试鉴定海岛棉的代表性结构变异（SVs），并揭示海岛棉的群体分化和适应性改良。

方法

通过对一个多年生 Gb 棉花品系（Gb_M210936）的基因组组装和比较基因组分析，将 Gb_M210936 与一年生 Gb 品系 3-79 和野生异源四倍体棉花 G. darwinii 进行比较，鉴定 Gb 棉花驯化过程中的变异。利用 6 个多年生 Gb 品系结合重新测序的 1129 个棉花品系进行群体和遗传分析。从种间渗入和种内倒位产生的大片段单倍型（haploblocks）被鉴定出来，并用于分析它们对海岛棉群体分化和农艺性状的影响。

结果

组装了一个多年生海岛棉的参考基因组。鉴定了海岛棉的代表性 SVs，并发现 31 个 SVs 与农艺性状相关。多年生 Gb 棉花与美洲起源的野生到地方品种连续体 Gb 棉花亲缘关系更近，Gb 棉花最初在那里被驯化。haploblocks 与海岛棉农艺性状的改良有关，促进了海岛棉分化为三个亚组，受到了育种选择的影响，可能推动 Gb 棉花适应中亚。