SNP discovery for genetic diversity and population structure analysis coupled with restriction-associated DNA (RAD) sequencing in walnut cultivars of Sichuan Province, China

The walnut is an excellent food product with abundant nutrients. However, the inference of its population structure has been hindered by the intricate phylogenetic relationships among <i>Juglans</i> species. In this study, RAD sequencing was conducted to investigate the genetic variation and population structure among 41 walnut cultivars from Southwestern Sichuan (SS, <i>n</i> = 10), Eastern Sichuan (ES, <i>n</i> = 26) and Northern China (NC, <i>n</i> = 5). The resulting 6357 single-nucleotide polymorphisms divided the 41 walnut cultivars into two major groups corresponding to the ES and SS gene pools, and NC was clustered with the ES1 subgroup. Additionally, two cultivars, WB01 and SMJ, were reclassified to correct their previous morphological classifications. The migration rate from ES to SS was greater than that in the reverse direction, and the genetic differentiation between the ES and SS populations was high. Moreover, the estimated expected heterozygosity (<i>H_e
</i> = 0.308) and polymorphism levels (<i>P_i
</i> (<i>π</i>) = 0.030) of the SS group were greater than those of the ES group. Similarly, the average genetic distance of the SS population (0.563) was higher than that of the ES population (0.522), and the rate of linkage disequilibrium decay in the SS population was faster. All the results indicate that the SS population has greater genetic diversity and is more primitive than the ES group. The present study provides a theoretical basis for the division, conservation, and utilization of walnut germplasm resources, and these findings can be applied in breeding programs to obtain high-quality cultivars of <i>Juglans</i>.

核桃是一类营养丰沛的优质食用佳品。然而，胡桃属（Juglans）物种间复杂的系统发育关系，阻碍了核桃种群遗传结构的解析。本研究采用RAD测序（RAD sequencing）技术，对来自四川西南部（SS，n=10）、四川东部（ES，n=26）以及中国北方（NC，n=5）的41份核桃栽培品种开展遗传变异与种群结构分析。最终获得的6357个单核苷酸多态性（single-nucleotide polymorphisms, SNP）位点将41份核桃栽培品种划分为两大类群，分别对应ES与SS基因库，其中NC类群与ES1亚群聚为一支。此外，本研究对WB01与SMJ两个栽培品种进行了重新分类，以修正此前基于形态学的分类结果。ES向SS的基因流强度高于反向的基因流，且ES与SS种群间的遗传分化程度较高。SS群体的期望杂合度（He=0.308）与多态性水平（Pi(π)=0.030）均高于ES群体。同理，SS群体的平均遗传距离（0.563）亦高于ES群体（0.522），且SS群体的连锁不平衡衰减速度更快。上述结果均表明，相较于ES群体，SS群体拥有更高的遗传多样性且演化地位更为原始。本研究为核桃种质资源的区划、保护与利用提供了理论依据，相关研究结果可应用于胡桃属（Juglans）优质栽培品种的育种工作中。