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Abstract：
Quinoa (Chenopodium quinoa) is a well-known climate-resilient crop and has been introduced into multiple marginal lands across the world, including China, to improve food security and/or balanced nutrient supplies. Conventional breeding has been widely applied in the selection and breeding of quinoa varieties in China since 1980s; however, few studies have been implemented on the genetic variances among different varieties developed by diversity breeding objectives. In this study, the phenotypic and genetic differences between two varieties (Longli-4 and CA3-1) from China were systematically analyzed. A total of 407,651 and 2,731,411 single nucleotide polymorphisms (SNPs) and 212,724 and 587,935 small insertion and deletion (INDELs) were detected for Longli-4 and CA3-1, respectively, when compared with the reference genome of PI614886. The SNPs/INDELs were unevenly distributed across each chromosome for both varieties. There were 143,996 SNPs and 83,410 INDELs shared between Longli-4 and CA3-1, accounting for 4% of the total variances. The variation was then screened based on the SNP effects. There were 818 and 73 genes with the variety-specific non-synonymous and stop-gain variation in Longli-4, whereas there were 13,701 and 733 genes in CA3-1. Specifically, 3501 genes with the non-synonymous variation and 74 genes with the stop-gain variation were found in both Longli-4 and CA3-1. These results suggest that convergent selection occurred during the different breeding processes. A set of candidate genes related to agronomic traits and domestication were further selected to detect the genetic divergence in detail in the two varieties. Only one domestication gene was identified having Longli-4-specific stop-gain variation. Twelve candidate genes related to betalain (1), flowering (4), seed size (2), domestication (1), and saponin (4) were identified having CA3-1-specific stop-gain variation. Interestingly, one seed size gene homologous of CKX1 (cytokinin oxidase/dehydrogenase 1) had the stop-gain variation in both varieties. This research will therefore provide guidance for the molecular-assisted breeding in quinoa.
摘要：
藜麦（藜麦）是一种众所周知的气候适应作物，已被引入世界各地的多个边缘土地，包括中国,改善粮食安全和/或均衡的营养供应。传统育种自20世纪80年代以来在我国藜麦品种选育中得到了广泛的应用,关于通过多样性育种目标开发的不同品种之间的遗传变异的研究很少。在这项研究中,系统分析了中国两个品种（Longli-4和CA3-1）的表型和遗传差异。Longli-4和CA3-1分别检测到407,651和2,731,411个单核苷酸多态性（SNPs）和212,724和587,935个小插入和缺失（INDEL），当与PI614886的参考基因组比较时。对于两个品种，SNP/INDEL在每个染色体上的分布不均匀。Longli-4和CA3-1共有143,996个SNP和83,410个INDEL，占总方差的4%。然后基于SNP效应筛选变异。Longli-4中有818和73个基因具有品种特异性非同义和停止增益变异，而CA3-1中有13701和733个基因。具体来说,在Longli-4和CA3-1中均发现了3501个具有非同义变异的基因和74个具有停止增益变异的基因。这些结果表明，在不同的育种过程中发生了趋同选择。进一步选择了一组与农艺性状和驯化有关的候选基因，以检测两个品种的详细遗传分歧。仅鉴定出一个具有Longli-4特异性停止增益变异的驯化基因。与betalain相关的十二个候选基因（1），开花（4），种子大小(2)，驯化（1），和皂苷(4)被鉴定为具有CA3-1特异性停止-增益变异。有趣的是,CKX1的一个种子大小同源基因（细胞分裂素氧化酶/脱氢酶1）在两个品种中均具有停止增益变异。本研究将为藜麦的分子辅助育种提供指导。
