Data_Sheet_1_Empirical phenotyping and genome-wide association study reveal the association of panicle architecture with yield in Chenopodium quinoa.docx

Chenopodium quinoa manifests adaptability to grow under varying agro-climatic scenarios. Assessing quinoa germplasm’s phenotypic and genetic variability is a prerequisite for introducing it as a potential candidate in cropping systems. Adaptability is the basic outcome of ecological genomics of crop plants. Adaptive variation predicted with a genome-wide association study provides a valuable basis for marker-assisted breeding. Hence, a panel of 72 quinoa plants was phenotyped for agro morphological attributes and association-mapping for distinct imperative agronomic traits. Inter simple sequence repeat (ISSR) markers were employed to assess genetic relatedness and population structure. Heatmap analysis showed three genotypes were early maturing, and six genotypes were attributed for highest yield. The SD-121-07 exhibited highest yield per plant possessing green, glomerulate shaped, compact density panicle with less leaves. However, SJrecm-03 yielded less exhibiting pink, intermediate shape, intermediate density panicles with less leaves. The phenotyping revealed strong correlation of panicle architecture with yield in quinoa. A genome-wide association study unraveled the associations between ISSR makers and agro-morphological traits. Mixed linear modes analysis yielded nine markers associated with eight traits at p ≤ 0.01. Moreover, ISSR markers significantly associated with panicle shape and leafiness were also associated with yield per plant. These findings contribute to the provision of authenticity for marker-assisted selection that ultimately would support quinoa breeding programs.

藜麦（Chenopodium quinoa）具备在不同农业气候情景下生长的适应性。评估藜麦种质资源的表型与遗传变异，是将其作为潜在候选作物引入种植系统的先决条件。适应性是作物生态基因组学的核心表征之一。通过全基因组关联分析（Genome-wide association study）预测得到的适应性变异，可为标记辅助育种提供宝贵的理论基础。为此，本研究对72份藜麦材料群体开展了农艺形态性状表型鉴定，并针对多项关键农艺性状进行关联作图分析。采用简单序列重复区间（Inter simple sequence repeat，ISSR）标记来评估藜麦的遗传亲缘关系与群体结构。热图分析结果显示，有3份基因型为早熟类型，另有6份基因型具有最高单株产量。其中，SD-121-07的单株产量最高，其具有绿色、团簇状、密度紧凑的穗状花序且叶片较少；而SJrecm-03的产量较低，其穗状花序呈粉红色、中间型、密度中等且叶片较少。表型鉴定结果表明，藜麦的穗部结构与单株产量存在显著相关性。全基因组关联分析揭示了ISSR标记与农艺形态性状之间的关联关系。混合线性模型分析在p≤0.01的显著性水平下，筛选出9个与8个性状相关的分子标记。此外，与穗部形状和叶片数量显著相关的ISSR标记，同样与单株产量存在关联。本研究结果可为标记辅助选择提供科学佐证，最终将为藜麦育种项目提供有力支撑。