Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China.
Rice Breeding and Genetics Section, Rice Research Institute, Kala Shah Kaku, Lahore, Pakistan.
Int J Mol Sci. 2019 Sep 28;20(19):4824. doi: 10.3390/ijms20194824.
The market success of any rice cultivar is exceedingly dependent on its grain appearance, as well as its grain yield, which define its demand by consumers as well as growers. The present study was undertaken to explore the contribution of nine major genes, , , , , , , , , and , in regulating four size and weight related traits, i.e., grain length (GL), grain width (GW), grain thickness (GT), and thousand grain weight (TGW) in 204 diverse rice germplasms using Insertion/Deletion (InDel) markers. The studied germplasm displayed wide-ranging variability in the four studied traits. Except for three genes, all six genes showed considerable association with these traits with varying strengths. Whole germplasm of 204 genotypes could be categorized into three major clusters with different grain sizes and weights that could be utilized in rice breeding programs where grain appearance and weight are under consideration. The study revealed that TGW was 24.9% influenced by GL, 37.4% influenced by GW, and 49.1% influenced by GT. Hence, assuming the trend of trait selection, i.e., GT > GW > GL, for improving TGW in the rice yield enhancement programs. The InDel markers successfully identified a total of 38 alleles, out of which 27 alleles were major and were found in more than 20 genotypes. GL was associated with four genes (, , , and ). GT was also found to be regulated by four different genes (, , , and ) out of the nine studied genes. GW was found to be under the control of three studied genes (, , and ), whereas TGW was found to be under the influence of four genes (, , , and ) in the germplasm under study. The Unweighted Pair Group Method with Arithmetic means (UPGMA) tree based on the studied InDel marker loci segregated the whole germplasm into three distinct clusters with dissimilar grain sizes and weights. A two-dimensional scatter plot constructed using Principal Coordinate Analysis (PCoA) based on InDel markers further separated the 204 rice germplasms into four sub-populations with prominent demarcations of extra-long, long, medium, and short grain type germplasms that can be utilized in breeding programs accordingly. The present study could help rice breeders to select a suitable InDel marker and in formulation of breeding strategies for improving grain appearance, as well as weight, to develop rice varieties to compete international market demands with higher yield returns. This study also confirms the efficient application of InDel markers in studying diverse types of rice germplasm, allelic frequencies, multiple-gene allele contributions, marker-trait associations, and genetic variations that can be explored further.
任何水稻品种的市场成功都极大地依赖于其谷物外观以及谷物产量，这决定了消费者和种植者对其的需求。本研究旨在利用插入/缺失（InDel）标记探索九个主要基因 、 、 、 、 、 、 、 和 对调节四个大小和重量相关性状的贡献，即粒长（GL）、粒宽（GW）、粒厚（GT）和千粒重（TGW）在 204 个不同的水稻种质中。研究的种质在四个研究性状中表现出广泛的变异性。除了三个基因外，所有六个基因都与这些性状有很大的关联，关联强度各不相同。整个 204 个基因型的种质可以分为三个主要的聚类，具有不同的粒大小和重量，可以在考虑谷物外观和重量的水稻育种计划中加以利用。研究表明，TGW 受 GL 影响 24.9%，受 GW 影响 37.4%，受 GT 影响 49.1%。因此，假设性状选择的趋势，即 GT>GW>GL，用于提高水稻产量提高计划中的 TGW。InDel 标记成功鉴定了总共 38 个等位基因，其中 27 个等位基因是主要的，存在于 20 多种基因型中。GL 与四个基因（ 、 、 和 ）有关。GT 也被发现受九个研究基因中的四个不同基因（ 、 、 和 ）调控。GW 受三个研究基因（ 、 和 ）控制，而 TGW 受研究种质中四个基因（ 、 、 和 ）的影响。基于研究 InDel 标记座的非加权对组平均法（UPGMA）树将整个种质分为三个具有不同粒大小和重量的不同聚类。基于 InDel 标记的主坐标分析（PCoA）构建的二维散点图进一步将 204 个水稻种质分为四个亚群，具有明显的超长、长、中、短粒型种质的划分，可相应用于育种计划。本研究可以帮助水稻育种者选择合适的 InDel 标记，并制定改良谷物外观和重量的育种策略，以开发具有更高产量回报的水稻品种来满足国际市场的需求。本研究还证实了 InDel 标记在研究不同类型水稻种质、等位基因频率、多基因等位基因贡献、标记-性状关联和遗传变异方面的有效应用，这些都可以进一步探索。
