Kumar Satish, Deng Cecilia Hong, Hunt Martin, Kirk Chris, Wiedow Claudia, Rowan Daryl, Wu Jun, Brewer Lester
Hawke's Bay Research Centre, The New Zealand Institute for Plant and Food Research Limited, Havelock North, New Zealand.
Mount Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.
Front Plant Sci. 2021 Jan 5;11:590846. doi: 10.3389/fpls.2020.590846. eCollection 2020.
Runs of homozygosity (ROH) have been widely used to study population history and trait architecture in humans and livestock species, but their application in self-incompatible plants has not been reported. The distributions of ROH in 199 accessions representing Asian pears (45), European pears (109), and interspecific hybrids (45) were investigated using genotyping-by-sequencing in this study. Fruit phenotypes including fruit weight, firmness, Brix, titratable acidity, and flavor volatiles were measured for genotype-phenotype analyses. The average number of ROH and the average total genomic length of ROH were 6 and 11 Mb, respectively, in Asian accessions, and 13 and 30 Mb, respectively, in European accessions. Significant associations between genomic inbreeding coefficients (F) and phenotypes were observed for 23 out of 32 traits analyzed. An overlap between ROH islands and significant markers from genome-wide association analyses was observed. Previously published quantitative trait loci for fruit traits and disease resistances also overlapped with some of the ROH islands. A prominent ROH island at the bottom of linkage group 17 overlapped with a recombination-supressed genomic region harboring the self-incompatibility locus. The observed ROH patterns suggested that systematic breeding of European pears would have started earlier than of Asian pears. Our research suggest that F would serve as a novel tool for managing inbreeding in gene-banks of self-incompatible plant species. ROH mapping provides a complementary strategy to unravel the genetic architecture of complex traits, and to evaluate differential selection in outbred plants. This seminal work would provide foundation for the ROH research in self-incompatible plants.
纯合性连续片段（ROH）已被广泛用于研究人类和家畜物种的种群历史及性状结构，但尚未见其在自交不亲和植物中的应用报道。本研究通过简化基因组测序对代表亚洲梨（45份）、欧洲梨（109份）和种间杂种（45份）的199份材料中的ROH分布进行了调查。对果实重量、硬度、糖度、可滴定酸度和风味挥发物等果实表型进行了测定，以进行基因型-表型分析。亚洲材料中ROH的平均数量和平均总基因组长度分别为6个和11 Mb，欧洲材料中分别为13个和30 Mb。在分析的32个性状中，有23个观察到基因组近亲繁殖系数（F）与表型之间存在显著关联。观察到ROH岛与全基因组关联分析中的显著标记之间存在重叠。先前发表的果实性状和抗病性数量性状位点也与一些ROH岛重叠。连锁群17底部一个显著的ROH岛与一个含有自交不亲和位点的重组抑制基因组区域重叠。观察到的ROH模式表明，欧洲梨的系统育种可能比亚洲梨开始得更早。我们的研究表明，F将作为一种管理自交不亲和植物物种基因库中近亲繁殖的新工具。ROH图谱提供了一种补充策略，用于揭示复杂性状的遗传结构，并评估远交植物中的差异选择。这项开创性工作将为自交不亲和植物的ROH研究奠定基础。
