Exploring the Genetic Characteristics of Two Recombinant Inbred Line Populations via High-Density SNP Markers in Maize

Understanding genetic characteristics can reveal the genetic diversity in maize and be used to explore evolutionary mechanisms and gene cloning. A high-density linkage map was constructed to determine recombination rates (RRs), segregation distortion regions (SDRs), and recombinant blocks (RBs) in two recombinant inbred line populations (RILs) (B73/By804 and Zong3/87-1) generated by the single seed descent method. Population B73/By804 containing 174 lines were genotyped with 198 simple sequence repeats (SSRs) markers while population Zong3/87-1 comprised of 175 lines, were genotyped with 210 SSR markers along with 1536 single nucleotide polymorphism (SNP) markers for each population, spanning 1526.7 cM and 1996.2 cM in the B73/By804 and Zong3/87-1 populations, respectively. The total variance of the RR in the whole genome was nearly 100 fold, and the maximum average was 10.43–11.50 cM/Mb while the minimum was 0.08–0.10 cM/Mb in the two populations. The average number of RB was 44 and 37 in the Zong3/87-1 and B73/By804 populations, respectively, whereas 28 SDRs were observed in both populations. We investigated 11 traits in Zong3/87-1 and 10 traits in B73/By804. Quantitative trait locus (QTLs) mapping of SNP+SSR with SNP and SSR marker sets were compared to showed the impact of different density markers on QTL mapping and resolution. The confidence interval of QTL Pa19 (FatB gene controlling palmitic acid content) was reduced from 3.5 Mb to 1.72 Mb, and the QTL Oil6 (DGAT1-2 gene controlling oil concentration) was significantly reduced from 10.8 Mb to 1.62 Mb. Thus, the use of high-density markers considerably improved QTL mapping resolution. The genetic information resulting from this study will support forthcoming efforts to understand recombination events, SDRs, and variations among different germplasm. Furthermore, this study will facilitate gene cloning and understanding of the fundamental sources of total variation and RR in maize, which is the most widely cultivated cereal crop.

解析遗传特征可揭示玉米的遗传多样性，为探究进化机制与基因克隆提供重要支撑。本研究构建了高密度遗传连锁图谱，用以分析两个通过单粒传法（single seed descent method）构建的重组自交系群体（recombinant inbred line populations, RILs）——B73/By804与Zong3/87-1——的重组率（recombination rates, RRs）、偏分离区域（segregation distortion regions, SDRs）与重组区块（recombinant blocks, RBs）。其中，B73/By804群体包含174个株系，采用198个简单序列重复（simple sequence repeats, SSRs）标记完成基因分型；Zong3/87-1群体包含175个株系，分别使用210个SSRs标记与1536个单核苷酸多态性（single nucleotide polymorphism, SNP）标记进行基因分型。两个群体的遗传图谱总长分别为1526.7 cM与1996.2 cM。全基因组范围内重组率的总变异幅度近100倍，两个群体的重组率最大值均值为10.43–11.50 cM/Mb，最小值均值为0.08–0.10 cM/Mb。Zong3/87-1与B73/By804群体的平均重组区块数量分别为44与37，且两个群体均检测到28个偏分离区域。本研究对Zong3/87-1群体的11个性状、B73/By804群体的10个性状开展了分析，对比仅使用SNP标记、仅使用SSRs标记以及联合使用SNP+SSRs标记的数量性状位点（quantitative trait locus, QTLs）定位结果，明确了不同密度标记对QTL定位精度与分辨率的影响。其中，控制棕榈酸含量的QTL Pa19（FatB基因）的置信区间从3.5 Mb缩小至1.72 Mb；控制籽粒含油量的QTL Oil6（DGAT1-2基因）的置信区间从10.8 Mb显著缩小至1.62 Mb，证实高密度标记可大幅提升QTL定位分辨率。本研究获得的遗传信息将为后续解析重组事件、偏分离区域以及不同种质间的遗传变异提供支撑。此外，本研究有助于推动玉米（全球种植最广泛的谷类作物）的基因克隆工作，加深对玉米总遗传变异与重组率根本来源的理解。