Exotic QTL improve grain quality in the tri-parental wheat population SW84

Developing the tri-parental exotic wheat population SW84
Genetic diversity of cultivated wheat was markedly reduced, first, during domestication and, second, since the onset of modern elite breeding. There is an increasing demand for utilizing genetic resources to increase genetic diversity and, simultaneously, to improve agronomic performance of cultivated wheat. To locate favorable effects of exotic wheat alleles, we developed the tri-parental wheat population SW84. The population was derived from crossing the hexaploid spring wheat cultivars Triso and Devon with one synthetic exotic donor accession, Syn084L, followed by two rounds of backcrossing and three rounds of selfing. SW84 consists of 359 BC2F4 lines, split into two families, D84 (Devon*Syn084L) and T84 (Triso*Syn084L).
Studying the genetic control of grain quality in SW84
As a case study, grain quality of SW84 was studied in replicated field trials. Transgressive segregation was observed for all studied grain quality traits by evaluating SW84 for two years at two locations under low and high nitrogen supply. Subsequently, a genome-wide association study (GWAS) was carried out based on genomic data derived from a 90k Infinium iSELECT single nucleotide polymorphism (SNP) array. In total, GWAS yielded 37 marker-trait associations, summarized to 16 quantitative trait loci (QTL). These SNPs indicate genetic regulators of grain protein content, grain hardness, sedimentation value and sedimentation ratio. The majority of exotic QTL alleles (75%) exerted favorable effects, increasing grain protein content and sedimentation value in ten and two cases, respectively. For instance, two exotic QTL alleles were associated with a substantial increase of grain protein content and sedimentation value by 1.09% and 7.31 ml, respectively. This finding confirms the potential of exotic germplasm to improve grain quality in cultivated wheat. So far, the molecular nature of most of the detected QTL is unknown. However, two QTL correspond to known genes controlling grain quality: The major QTL on chromosome 6B, increasing grain protein content by 0.70%, on average, co-localizes with the NAM-B1 gene, known to control grain protein content as well as iron and zinc content. Likewise, the major QTL on chromosome 5D, reducing grain hardness by 8.98%, on average, co-localizes with the gene for puroindoline b (Pinb-D1) at the Ha locus. In total, 13 QTL were detected across families, whereas one and three QTL were exclusively detected in families D84 and T84, respectively. Likewise, ten QTL were detected across nitrogen treatments, whereas one and five QTL were exclusively detected under low and high N treatments, respectively. Our data indicate that most effects in SW84 act across families and N levels. Merging of data from two families or two N treatments may, thus, be considered in association studies to increase sample size and, as a result, QTL detection power.
Utilizing favorable exotic QTL alleles in wheat breeding
Our study serves as a model how favorable exotic QTL alleles can be located in exotic germplasm of wheat. In future, the localized favorable exotic QTL alleles will be utilized in wheat breeding programs to simultaneously improve grain quality and selectively expand genetic diversity of the elite wheat gene pool.

构建三亲本外源小麦群体SW84

栽培小麦的遗传多样性在驯化过程中显著降低，且自现代优良品种育种启动以来进一步缩减。当前，科研界对利用遗传资源提升栽培小麦遗传多样性、同时改良其农艺性状的需求日益增长。为挖掘外源小麦等位基因的优良效应，本研究构建了三亲本小麦群体SW84。该群体由六倍体春小麦品种Triso与Devon，以及人工合成外源供体材料Syn084L杂交后，历经两轮回交与三轮自交获得。SW84群体包含359个BC2F4株系，分为两个亚群：D84（Devon×Syn084L）与T84（Triso×Syn084L）。

解析SW84的籽粒品质遗传调控机制

作为案例研究，本研究通过重复田间试验对SW84群体的籽粒品质进行了分析。本研究在两个地点、两种氮素水平（低氮与高氮）下对SW84开展了两年的表型鉴定，结果显示所有被测籽粒品质性状均出现超亲分离现象。随后，基于90k Infinium iSELECT单核苷酸多态性（single nucleotide polymorphism, SNP）芯片的基因组数据，本研究开展了全基因组关联分析（genome-wide association study, GWAS）。本次GWAS共检测到37个标记-性状关联位点，可整合为16个数量性状位点（quantitative trait loci, QTL）。这些SNP位点对应籽粒蛋白含量、籽粒硬度、沉降值及沉降比的遗传调控因子。其中75%的外源QTL等位基因具有优良效应：分别有10个和2个位点可提升籽粒蛋白含量与沉降值。例如，两个外源QTL等位基因可分别使籽粒蛋白含量提升1.09%、沉降值增加7.31 ml，效应显著。该结果证实了外源种质资源在改良栽培小麦籽粒品质方面的应用潜力。截至目前，绝大多数已检测到的QTL的分子本质仍未明确，但其中两个QTL与已知的籽粒品质调控基因共定位：位于6B染色体的主效QTL平均可使籽粒蛋白含量提升0.70%，其与NAM-B1基因共定位，该基因已知可调控籽粒蛋白含量以及铁、锌元素含量。同样，位于5D染色体的主效QTL平均可降低籽粒硬度8.98%，其与Ha位点上的puroindoline b（Pinb-D1）基因共定位。总体而言，13个QTL在两个亚群中均被检测到，另有1个和3个QTL仅分别在D84与T84亚群中被检出。同样，10个QTL在两种氮素处理下均被检测到，另有1个和5个QTL仅分别在低氮与高氮处理下被检出。本研究数据表明，SW84群体中的多数QTL效应在亚群间与氮素水平间均具有一致性。因此，在后续关联分析研究中，可考虑合并两个亚群或两种氮素处理的表型数据以扩大样本量，进而提升QTL检测效力。

在小麦育种中利用优良外源QTL等位基因

本研究为在小麦外源种质中挖掘优良外源QTL等位基因提供了示范范式。未来，可将已定位的优良外源QTL等位基因应用于小麦育种项目，以同步改良籽粒品质并定向扩充优良小麦基因库的遗传多样性。