Abstract: Chlorophyll is a key pigment involved in photosynthesis and influences plant photosynthetic efficiency and yield. However，the genetic basis underlying chlorophyll biosynthesis and regulation remains poorly understood. To dissect the genetic basis of chlorophyll content in soybean leaves，we used 563 accessions of a soybean natural population and evaluated their chlorophyll content at the flowering stage across three locations［Xinxiang City（Yuanyang County），Luohe City，and Xinyang City in Henan Province］.Based on genotype data from the GenoBaits Soybean 10K Panel，STRUCTURE analysis and phylogenetic tree analysis revealed significant subpopulation strucure（K=5）.In the subsequent genome⁃wide association study，four analytical models were constructed to identify significant single nucleotide polymorphism（SNP）loci.As a result，MLM，BLINK，MLMM and FarmCPU identified 15,9,5 and 4 significant loci，respectively.Among these，Gm04623 on chromosome 2 showed the strongest effect and was stably detected in all four models，explaining 9.77%—13.81% of the phenotypic variation.Through functional annotation and expression profile analysis of genes within the 300 kb region flanking Gm04623，we inferred that Glyma. 02g305400 was involved in regulating chlorophyll content in soybean leaves.This gene encoded a chlorophyll a/b binding protein that formed a complex with chlorophyll to capture light energy for photosynthesis. Haplotype analysis of the linkage block harboring this gene identified four haplotypes，among which H001 showed the highest chlorophyll content and significant differences from the others. This study detected major associated loci Gm04623 and the key candidate gene Glyma.02g305400 controlling chlorophyll content in soybean leaves，enriching the genetic understanding of this trait. The superior haplotype H001 with high chlorophyll content was also identified，providing genetic resources and theoretical support for molecular breeding of soybeans with high photosynthetic efficiency.

Key words: Soybean, Chlorophyll content, Population structure, Genome?wide association analysis, Haplotype analysis

摘要： 叶绿素是参与光合作用的重要细胞色素，影响植物的光合效率和产量，然而其合成及调控的遗传基础仍知之甚少。为解析大豆叶片叶绿素含量的遗传基础，利用563份大豆自然群体材料在河南省新乡市（原阳县）、漯河市和信阳市3个地点的盛花期叶绿素相对含量数据，基于GenoBaits Soybean 10KPanel芯片的基因型数据，通过STRUCTURE分析和系统发育树分析，揭示群体存在显著的亚群结构（K=5）。在后续全基因组关联分析中，构建4种模型来挖掘显著单核苷酸多态性（SNP）位点。结果显示，使用MLM、BLINK、MLMM、FarmCPU 模型分别获得15、9、5、4 个显著位点；其中位于2 号染色体上的Gm04623位点效应最强，在所有模型中均被检测到且是最显著位点，可解释表型变异的9.77%~13.81%。通过对该位点上下游共300 kb区间内基因的功能注释和表达谱分析，推测基因Glyma.02g305400参与调控大豆叶片叶绿素含量，该基因编码叶绿素a/b结合蛋白，通过与叶绿素结合形成蛋白复合体，捕获光能参与光合作用。该基因所在连锁区段的单倍型分析显示，存在4种单倍型，其中H001的叶绿素含量最高，且与其他单倍型存在显著差异。本研究检测到大豆叶片叶绿素含量主效关联位点Gm04623与关键候选基因Glyma.02g305400，丰富了其遗传调控基础，并筛选出高叶绿素含量优势单倍型H001，为大豆高光效分子育种提供了基因资源与理论支撑。

关键词: 大豆, 叶绿素含量, 群体结构, 全基因组关联分析, 单倍型分析