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Background <p>Genetic diversity of crop is crucial for improving breeding programs and for the development of new cultivars.</p> Methods and Results <p>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).</p> Conclusion <p>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.</p>

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Molecular genetic diversity estimates and identification of multilocus fine and coarse rice genotypes using microsatellite markers

  • 期刊论文

  • 发表日期：

    2025年6月23日

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  • Ayesha Wadood,
  • Amjad Hameed,
  • Zia ul Qamar

摘要

Background

Genetic diversity of crop is crucial for improving breeding programs and for the development of new cultivars.

Methods and Results

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).

Conclusion

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.