Genome-wide association for agro-morphological traits in a triploid banana population with large chromosome rearrangements

IF 8.7 1区 农林科学 Q1 Agricultural and Biological Sciences Horticulture Research Pub Date : 2024-11-07 DOI:10.1093/hr/uhae307
S Rio, L Toniutti, F Salmon, C Hervouet, C Cardi, P Mournet, C Guiougou, F Marius, C Mina, J M Delos, F Lambert, C Madec, J C Efile, C Cruaud, J M Aury, A D’Hont, J Y Hoarau, G Martin
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Abstract

Banana breeding is hampered by the very low fertility of domesticated bananas and the lack of knowledge about the genetic determinism of agronomic traits. We analysed a breeding population of 2 723 triploid hybrids resulting from crosses between diploid and tetraploid M. acuminata parents, which was evaluated over three successive crop-cycles for 24 traits relating to yield components and plant, bunch and fruit architectures. A subset of 1 129 individuals was genotyped-by-sequencing revealing 205 612 single nucleotide polymorphisms. Most parents were heterozygous for one or several large reciprocal chromosomal translocations, which are known to impact recombination and chromosomal segregation. We applied two linear mixed models to detect associations between markers and traits: (i) a standard model with a kinship calculated using all SNPs and (ii) a model with chromosome-specific kinships that aims at recovering statistical power at alleles carried by long non-recombined haplotypic segments. For 23 of the 24 traits, we identified one to five significant quantitative trait loci (QTLs) for which the origin of favourable alleles could often be determined among the main ancestral contributors to banana cultivars. Several QTLs, located in the rearranged regions, were only detected using the second model. The resulting QTL landscape represents an important resource to support breeding programs. The proposed strategy for recovering power at SNPs carried by long non-recombined rearranged haplotypic segments is an important methodological advance for future association studies in banana and other species affected by chromosomal rearrangements.
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染色体大重排的三倍体香蕉群体农业形态特征的全基因组关联研究
由于驯化香蕉的生育率非常低,而且对农艺性状的遗传决定性缺乏了解,香蕉育种受到了阻碍。我们分析了一个由 2 723 个三倍体杂交种组成的育种群体,这些杂交种是由二倍体和四倍体 M. acuminata 亲本杂交产生的,在连续三个作物周期中对这些杂交种的 24 个性状进行了评估,这些性状涉及产量成分以及植株、果穗和果实的结构。对 1 129 个个体的子集进行了基因分型测序,发现了 205 612 个单核苷酸多态性。大多数亲本都是一个或多个大型互易染色体易位的杂合子,众所周知,这些易位会影响重组和染色体分离。我们采用了两种线性混合模型来检测标记与性状之间的关联:(i) 使用所有 SNP 计算亲缘关系的标准模型;(ii) 染色体特异性亲缘关系模型,旨在恢复非重组单倍型长片段所携带等位基因的统计能力。对于 24 个性状中的 23 个性状,我们确定了 1 至 5 个重要的数量性状位点(QTL),这些位点的有利等位基因的来源往往可以在香蕉栽培品种的主要祖先贡献者中确定。有几个 QTL 位于重新排列的区域,只有在第二个模型中才能检测到。由此产生的 QTL 图谱是支持育种计划的重要资源。所提出的恢复非重组重排单倍型长片段所携带的 SNPs 功率的策略,是未来香蕉和其他受染色体重排影响的物种进行关联研究的重要方法学进步。
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来源期刊
Horticulture Research
Horticulture Research Biochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
11.20
自引率
6.90%
发文量
367
审稿时长
20 weeks
期刊介绍: Horticulture Research, an open access journal affiliated with Nanjing Agricultural University, has achieved the prestigious ranking of number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. As a leading publication in the field, the journal is dedicated to disseminating original research articles, comprehensive reviews, insightful perspectives, thought-provoking comments, and valuable correspondence articles and letters to the editor. Its scope encompasses all vital aspects of horticultural plants and disciplines, such as biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.
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