Wadood Ayesha, Hameed Amjad, Ul Qamar Zia
Marker Assisted Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan.
Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan.
Mol Biol Rep. 2025 Jun 23;52(1):631. doi: 10.1007/s11033-025-10732-8.
Genetic diversity of crop is crucial for improving breeding programs and for the development of new cultivars.
This study aimed to identify unique multilocus genotypes (MLGs) and to assess genetic diversity within 11 rice (6 coarse rice varieties (non-aromatic with shorter and broader grains) and 5 fine rice varieties (typically aromatic with long and slender grains)) accessions using 50 SSR markers. Polymorphism information content (PIC) value was used to determine the number of polymorphic markers and discriminant analysis of principal components (DAPC) along with hierarchical clustering were used to identify closely related genotypes. Results were further validated by filtering multilocus genotypes using the mlg.filter function of poppr package in R software. Moreover, genetic diversity parameters were calculated and AMOVA was performed to evaluate variance within and between fine and coarse rice varieties. Among 50 SSR markers, 13 SSR markers (RM259, RM7075, RM262, RM55, RM520, RM255, RM252, RM190, RM248, RM427, RM336, RM205, and RM286) exhibited high polymorphism (PIC 0.50). DAPC and hierarchical clustering showed 4 closely related genotypes (NIAB_HT-18 and Super Basmati in fine rice, and KSK-133 and KS-282 in coarse rice) with 63.7% unique and 36.3% closely related MLGs. AMOVA revealed significant differentiation between fine and coarse rice varieties (62.2% within populations, 25.5% between samples within populations).
In conclusion, this study underscored the evaluation of molecular genetic diversity and identification of unique multilocus fine and coarse rice genotypes. Furthermore, present findings will facilitate DNA fingerprinting in rice processes essential for identifying distinctness in candidate varieties, ensuring accurate varietal identification and approval.
作物的遗传多样性对于改进育种计划和培育新品种至关重要。
本研究旨在利用50个SSR标记鉴定独特的多位点基因型（MLGs），并评估11份水稻种质（6份粗稻品种（非香稻，粒短而宽）和5份细稻品种（典型香稻，粒长而细））的遗传多样性。利用多态性信息含量（PIC）值确定多态性标记的数量，并使用主成分判别分析（DAPC）和层次聚类来鉴定亲缘关系较近的基因型。通过使用R软件中poppr包的mlg.filter函数过滤多位点基因型，进一步验证了结果。此外，计算了遗传多样性参数，并进行了分子方差分析（AMOVA）以评估细稻和粗稻品种内部和之间的方差。在50个SSR标记中，13个SSR标记（RM259、RM7075、RM262、RM55、RM520、RM255、RM252、RM190、RM248、RM427、RM336、RM205和RM286）表现出高度多态性（PIC>0.50）。DAPC和层次聚类显示4个亲缘关系较近的基因型（细稻中的NIAB_HT - 18和超级巴斯马蒂，粗稻中的KSK - 133和KS - 282），其中63.7%为独特的MLGs，36.3%为亲缘关系较近的MLGs。AMOVA揭示了细稻和粗稻品种之间存在显著差异（群体内62.2%，群体内样本间25.5%）。
总之，本研究强调了对分子遗传多样性的评估以及对独特的多位点细稻和粗稻基因型的鉴定。此外，目前的研究结果将有助于水稻过程中的DNA指纹识别，这对于鉴定候选品种的特异性、确保准确的品种鉴定和批准至关重要。
