QTL and genetic map for 2018.

Nitrogen (N), phosphorus (P), and sulfur (S) are essential nutrients for plant health. Deficiencies in N, P, or S in plants lead to lower seed production and seed quality in grain crops, including soybean seed. Soybean seed is a source of protein, oil, essential amino acids, and minerals. These nutrients are essential for plant health, and maintaining N, P, and S levels in soybean seed is crucial for higher seed nutritional value and amino acids quality. There is limited information on genomic regions, candidate genes, and molecular markers associated with soybean seed N, P, and S. Two field experiments were carried out in two locations using a ‘Forrest’ × ‘Williams 82’ recombinant inbred lines (RIL) population. A 306 RIL population and 2075 SNP markers were used to create the genetic map. The results showed a wide range of N, P, and S concentrations in both locations among RIL population lines. Based on the broad-sense heritability (H2), 91.7% of seed N concentration variation was due to genetic effects, followed by 48.2% for S seed concentration, and a heritability of close to zero for seed P concentration. Eleven QTL were identified for seed N, seven QTL for seed P, and nine QTL for seed S in two locations. All these QTL had a significant linkage to the trait as their LOD ranged from 2.5 to 6.48 in 2018 and from 2.75 to 128.72 in 2020. Two QTL for seed N (qN-02-[IL-2020] on Chr 4, and qN-03-[IL-2020] on Chr 4 were identified at the marker Gm04_4687302-Gm04_7672403 and Gm04_7672403, and their LOD were 45.06 and 96.98, and their contribution to the phenotypic variation were 45.85% and 48.37%, respectively. The low heritability of P indicated a major interactions between the trait (P) and environment. Except for the seed N, P, and S QTL, identified on Chr 16, 11 QTL reported here were not previously identified and therefore are novel. Several functional genes encoding N-, P-, and S-proteins, enzymes, and transporters were identified and located within the QTL interval. To our knowledge, the QTL identified here on Chr 2 and 6 are novel and were not previously identified. Therefore, QTL, genes, and molecular markers discovered in this research will provide breeders with new knowledge and tools for soybean selection for optimum seed mineral nutritional qualities. Also, this new findings advance our knowledge of physiology and genetics of seed N, S, and P candidate genes for genetic engineering application.

氮（Nitrogen, N）、磷（Phosphorus, P）和硫（Sulfur, S）是植物健康生长所必需的营养元素。植物缺乏这三种元素会降低包括大豆种子在内的谷类作物的种子产量与品质。大豆种子是蛋白质、油脂、必需氨基酸与矿物质的重要来源。上述营养元素对植物健康至关重要，维持大豆种子中氮、磷、硫的含量水平，对提升种子营养价值与氨基酸品质具有关键作用。

目前关于与大豆种子氮、磷、硫含量相关的基因组区域、候选基因及分子标记的研究信息较为有限。本研究采用‘Forrest’בWilliams 82’重组自交系（recombinant inbred lines, RIL）群体，在两个试验地点开展了两项田间试验。研究使用306个RIL群体材料与2075个单核苷酸多态性（single nucleotide polymorphism, SNP）标记构建了遗传图谱。

结果显示，两个试验地点的RIL群体家系间，种子氮、磷、硫浓度均存在广泛的变异。基于广义遗传力（broad-sense heritability, H²）分析，种子氮浓度变异中有91.7%源于遗传效应，其次为种子硫浓度的48.2%，而种子磷浓度的遗传力近乎为0。

在两个地点共鉴定到11个与种子氮含量相关的数量性状位点（quantitative trait locus, QTL）、7个与种子磷含量相关的QTL以及9个与种子硫含量相关的QTL。所有上述QTL均与目标性状存在显著连锁关系：2018年其似然比对数分值（logarithm of odds, LOD）范围为2.5~6.48，2020年则为2.75~128.72。

其中，2个与种子氮含量相关的QTL（Chr 4上的qN-02-[IL-2020]与qN-03-[IL-2020]）被定位在标记区间Gm04_4687302-Gm04_7672403与Gm04_7672403内，其LOD值分别为45.06与96.98，对表型变异的解释率分别为45.85%与48.37%。

种子磷含量的低遗传力表明该性状与环境间存在较强的互作效应。除了定位于Chr 16上的种子氮、磷、硫QTL外，本研究报道的其余11个QTL均为首次鉴定的新位点。此外，在这些QTL区间内还鉴定到多个编码氮、磷、硫相关蛋白、酶及转运蛋白的功能基因。

据我们所知，本研究在Chr 2与Chr 6上鉴定到的QTL均为全新的未被报道过的位点。因此，本研究发现的QTL、基因及分子标记将为育种家选育最优种子矿质营养品质的大豆品种提供新的理论依据与工具。同时，这些新发现也加深了我们对种子氮、硫、磷候选基因的生理学与遗传学认知，可用于基因工程相关研究。