Zhang Qianqian, Lv Wenjun, Liu Defu, Xie Xueying, Yang Ke, Tang You, Solkner Johann
School of Chemical and Biological Engineering, University of Science and Technology, Beijing, China.
Department of Agriculture, University of Natural Resources and Life Sciences Vienna BOKU, Vienna, Austria.
BMC Genomics. 2025 May 14;26(1):481. doi: 10.1186/s12864-025-11674-y.
Runs of homozygosity (ROH) have been extensively investigated to uncover the genomic inbred regions that reflect past population and breeding histories. In this study, we have explored the distribution and number of ROH in different Lactuca species including the cultivated lettuce varieties and their wild relatives. Next generation sequencing (NGS) technology provides the unique opportunity to study the genomes with resolution up to per-base-pair and we could compute ROH in the highest accuracy using NGS data. Our study reveals that Lactuca sativa has the longest average ROH length and fewest number of ROHs, while wild species show shorter, more numerous ROHs as expected. We found that these cultivated varieties exhibit relatively stable number of ROH and ROH lengths, with the largest median ROH count observed in Oilseed and the largest average ROH length in Crisphead. There is a significant proportion of medium-length ROHs (100 kb-1 Mb) enriched in L. sativa and L. serriola, with the highest number observed in L. serriola, while L. saligna has more short ROHs (< 10 KB), and the highest number of ROHs in the 10 KB-100 KB range were observed in Butterhead, with Stalk and Oilseed showing fewer and shorter ROHs overall. It suggests that Stalk and Oilseed were still in a process of breeding. The comparison between PLINK computation and our developed in-house algorithm shows that PLINK tends to detect longer ROH, whereas our algorithm adopts a more conservative approach, resulting in fewer and shorter ROH segments detected with higher precision more suitable for NGS data. We further analyze the distribution of ROH hotspots with a higher frequency occurred across cultivated species genomes, which has identified key genes such as DREB2B, NHL12, RPV1, and EIX2, which play crucial roles in plant stress tolerance and immune responses, enhancing adaptability to extreme environments and providing resistance to various diseases. These findings provide fresh scientific insights into lettuce breeding, germplasm conservation, and sustainable production, highlighting the importance of understanding and managing genetic diversity in global agricultural practices.
纯合性连续片段（ROH）已被广泛研究，以揭示反映过去种群和育种历史的基因组自交区域。在本研究中，我们探索了不同莴苣物种（包括栽培生菜品种及其野生近缘种）中ROH的分布和数量。下一代测序（NGS）技术提供了以单碱基对分辨率研究基因组的独特机会，并且我们可以使用NGS数据以最高精度计算ROH。我们的研究表明，栽培生菜（Lactuca sativa）的平均ROH长度最长，ROH数量最少，而野生种如预期的那样显示出较短且数量更多的ROH。我们发现这些栽培品种的ROH数量和ROH长度相对稳定，在油用生菜中观察到的ROH中位数最大，在结球生菜中平均ROH长度最大。有相当比例的中等长度ROH（100 kb - 1 Mb）在栽培生菜和刺叶莴苣（L. serriola）中富集，在刺叶莴苣中观察到的数量最多，而柳叶莴苣（L. saligna）有更多短ROH（< 10 KB），在奶油生菜中观察到10 KB - 100 KB范围内的ROH数量最多，茎用生菜和油用生菜总体上显示出更少且更短的ROH。这表明茎用生菜和油用生菜仍处于育种过程中。PLINK计算与我们开发的内部算法之间的比较表明，PLINK倾向于检测到更长的ROH，而我们的算法采用更保守的方法，导致检测到更少且更短的ROH片段，但精度更高，更适合NGS数据。我们进一步分析了在栽培物种基因组中出现频率较高的ROH热点的分布，确定了关键基因，如DREB2B、NHL12、RPV1和EIX2，这些基因在植物胁迫耐受性和免疫反应中起关键作用，增强了对极端环境的适应性并提供了对各种疾病的抗性。这些发现为生菜育种、种质保护和可持续生产提供了新的科学见解，突出了在全球农业实践中理解和管理遗传多样性的重要性。
