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.

中文翻译：

---

具有大染色体重排的三倍体香蕉种群中农业形态学性状的全基因组关联


香蕉育种受到驯化香蕉生育率非常低的阻碍，并且缺乏关于农艺性状遗传决定论的知识。我们分析了二倍体和四倍体 M. acuminata 亲本杂交产生的 2 723 个三倍体杂交种群，在三个连续的作物周期中评估了与产量成分和植物、串和果实结构相关的 24 个性状。通过测序对 1 129 个个体的子集进行基因分型，揭示了 205 612 个单核苷酸多态性。大多数父母是一个或多个大的相互染色体易位的杂合子，已知这些易位会影响重组和染色体分离。我们应用了两个线性混合模型来检测标记和性状之间的关联：（i） 一个标准模型，使用所有 SNP 计算亲缘关系，以及 （ii） 一个具有染色体特异性亲缘关系的模型，旨在恢复长非重组单倍型片段携带的等位基因的统计能力。对于 24 个性状中的 23 个，我们确定了 1 到 5 个重要的数量性状位点 （QTL），这些位点的有利等位基因的起源通常可以在香蕉品种的主要祖先贡献者中确定。位于重排区域的几个 QTL 仅使用第二个模型检测到。由此产生的 QTL 景观代表了支持育种计划的重要资源。所提出的恢复长非重组重排单倍型片段携带的 SNP 力量的策略是未来香蕉和其他受染色体重排影响的物种关联研究的重要方法学进步。