Genome-wide artificial introgressions of Gossypium barbadense into G. hirsutum reveal superior loci for simultaneous improvement of cotton fiber quality and yield traits,Journal of Advanced Research

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Genome-wide artificial introgressions of Gossypium barbadense into G. hirsutum reveal superior loci for simultaneous improvement of cotton fiber quality and yield traits
Journal of Advanced Research ( IF 11.4 ) Pub Date : 2022-11-30 , DOI: 10.1016/j.jare.2022.11.009
Shaoqi Li ₁ , Linglei Kong ₂ , Xianghui Xiao ₂ , Pengtao Li ₃ , Aiying Liu ₂ , Junwen Li ₂ , Juwu Gong ₂ , Wankui Gong ₂ , Qun Ge ₂ , Haihong Shang ₂ , Jingtao Pan ₂ , Hong Chen ₄ , Yan Peng ₅ , Yuanming Zhang ₆ , Quanwei Lu ₃ , Yuzhen Shi ₂ , Youlu Yuan ₁

Affiliation

Introduction

The simultaneous improvement of fiber quality and yield for cotton is strongly limited by the narrow genetic backgrounds of Gossypium hirsutum (Gh) and the negative genetic correlations among traits. An effective way to overcome the bottlenecks is to introgress the favorable alleles of Gossypium barbadense (Gb) for fiber quality into Gh with high yield.

Objectives

This study was to identify superior loci for the improvement of fiber quality and yield.

Methods

Two sets of chromosome segment substitution lines (CSSLs) were generated by crossing Hai1 (Gb, donor-parent) with cultivar CCRI36 (Gh) and CCRI45 (Gh) as genetic backgrounds, and cultivated in 6 and 8 environments, respectively. The kmer genotyping strategy was improved and applied to the population genetic analysis of 743 genomic sequencing data. A progeny segregating population was constructed to validate genetic effects of the candidate loci.

Results

A total of 68,912 and 83,352 genome-wide introgressed kmers were identified in the CCRI36 and CCRI45 populations, respectively. Over 90 % introgressions were homologous exchanges and about 21 % were reverse insertions. In total, 291 major introgressed segments were identified with stable genetic effects, of which 66(22.98 %), 64(21.99 %), 35(12.03 %), 31(10.65 %) and 18(6.19 %) were beneficial for the improvement of fiber length (FL), strength (FS), micronaire, lint-percentage (LP) and boll-weight, respectively. Thirty-nine introgression segments were detected with stable favorable additive effects for simultaneous improvement of 2 or more traits in Gh genetic background, including 6 could increase FL/FS and LP. The pyramiding effects of 3 pleiotropic segments (A07:C45Clu-081, D06:C45Clu-218, D02:C45Clu-193) were further validated in the segregating population.

Conclusion

The combining of genome-wide introgressions and kmer genotyping strategy showed significant advantages in exploring genetic resources. Through the genome-wide comprehensive mining, a total of 11 clusters (segments) were discovered for the stable simultaneous improvement of FL/FS and LP, which should be paid more attention in the future.

中文翻译：

海岛棉全基因组人工渗入陆地棉揭示了同时改善棉纤维品质和产量性状的优越位点

介绍

棉花纤维品质和产量的同时提高受到陆地棉（Gh）狭窄的遗传背景和性状之间的负遗传相关性的严重限制。克服这一瓶颈的有效方法是将海岛棉( Gb )对纤维品质有利的等位基因导入Gh，并获得高产。

目标

本研究旨在确定提高纤维质量和产量的优良基因座。

方法

通过 Hai1（ Gb，供体亲本）与品种 CCRI36（Gh）和 CCRI45（Gh ）作为遗传背景杂交产生两组染色体片段替换系（CSSL），并分别在 6 和 8 环境中培养。改进kmer基因分型策略，应用于743个基因组测序数据的群体遗传分析。构建后代分离群体以验证候选基因座的遗传效应。

结果

在 CCRI36 和 CCRI45 群体中分别鉴定出总共 68,912 和 83,352 个全基因组渗入 kmers。超过 90% 的渗入是同源交换，约 21% 是反向插入。总共鉴定出291个具有稳定遗传效应的主要渗入片段，其中66个(22.98%)、64个(21.99%)、35个(12.03%)、31个(10.65%)和18个(6.19%)有利于改善。分别为纤维长度 (FL)、强度 (FS)、马克隆值、绒毛百分比 (LP) 和棉铃重量。检测到 39 个基因渗入片段，具有稳定的有利加性效应，可同时改善Gh遗传背景中的 2 个或多个性状，其中 6 个可以增加 FL/FS 和 LP。3 个多效性片段（A07:C45Clu-081、D06:C45Clu-218、D02:C45Clu-193）的金字塔效应在隔离群体中得到进一步验证。