Department of Soil and Crop Sciences, Texas A&M University, Agronomy Field Lab 110/111, College Station, TX, 77843, USA.
Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Theor Appl Genet. 2023 Jun 17;136(7):155. doi: 10.1007/s00122-023-04394-y.
A novel locus was discovered on chromosome 7 associated with a lesion mimic in maize; this lesion mimic had a quantitative and heritable phenotype and was predicted better via subset genomic markers than whole genome markers across diverse environments. Lesion mimics are a phenotype of leaf micro-spotting in maize (Zea mays L.), which can be early signs of biotic or abiotic stresses. Dissecting its inheritance is helpful to understand how these loci behave across different genetic backgrounds. Here, 538 maize recombinant inbred lines (RILs) segregating for a novel lesion mimic were quantitatively phenotyped in Georgia, Texas, and Wisconsin. These RILs were derived from three bi-parental crosses using a tropical pollinator (Tx773) as the common parent crossed with three inbreds (LH195, LH82, and PB80). While this lesion mimic was heritable across three environments based on phenotypic ([Formula: see text] = 0.68) and genomic ([Formula: see text] = 0.91) data, transgressive segregation was observed. A genome-wide association study identified a single novel locus on chromosome 7 (at 70.6 Mb) also covered by a quantitative trait locus interval (69.3-71.0 Mb), explaining 11-15% of the variation, depending on the environment. One candidate gene identified in this region, Zm00001eb308070, is related to the abscisic acid pathway involving in cell death. Genomic predictions were applied to genome-wide markers (39,611 markers) contrasted with a marker subset (51 markers). Population structure explained more variation than environment in genomic prediction, but other substantial genetic background effects were additionally detected. Subset markers explained substantially less genetic variation (24.9%) for the lesion mimic than whole genome markers (55.4%) in the model, yet predicted the lesion mimic better (0.56-0.66 vs. 0.26-0.29). These results indicate this lesion mimic phenotype was less affected by environment than by epistasis and genetic background effects, which explain its transgressive segregation.
一个新的基因座被发现在 7 号染色体上与玉米中的损伤模拟相关；该损伤模拟具有定量的和可遗传的表型，并且通过跨多种环境的子集基因组标记预测优于全基因组标记。损伤模拟是玉米（Zea mays L.）叶片微斑的表型，它可能是生物或非生物胁迫的早期迹象。剖析其遗传有助于了解这些基因座在不同遗传背景下的行为。在这里，538 个玉米重组自交系（RIL）在佐治亚州、德克萨斯州和威斯康星州被定量表型为一种新的损伤模拟。这些 RIL 是由三个双亲杂交产生的，使用热带授粉者（Tx773）作为共同亲本与三个自交系（LH195、LH82 和 PB80）杂交。虽然基于表型（[Formula: see text] = 0.68）和基因组（[Formula: see text] = 0.91）数据，这种损伤模拟在三个环境中是可遗传的，但观察到了超亲分离。全基因组关联研究在染色体 7 上（在 70.6 Mb 处）鉴定到一个单一的新基因座，也被一个数量性状基因座区间（69.3-71.0 Mb）覆盖，根据环境的不同，解释了 11-15%的变异。在这个区域中鉴定到的一个候选基因，Zm00001eb308070，与涉及细胞死亡的脱落酸途径有关。基因组预测被应用于全基因组标记（39611 个标记）与标记子集（51 个标记）。群体结构比环境对基因组预测解释的变异更多，但另外还检测到了其他重要的遗传背景效应。在模型中，与全基因组标记（55.4%）相比，子集标记对损伤模拟的解释要差得多（24.9%），但预测得更好（0.56-0.66 与 0.26-0.29）。这些结果表明，这种损伤模拟表型受环境的影响小于受上位性和遗传背景效应的影响，这解释了它的超亲分离。
