Muhammad Ashfaq1, Abdul Rasheed2, Muhammad Sajjad3, Muhammad Ali4,5, Bilal Rasool6, Muhammad Arshad Javed2, Sami Ul Allah7, Shabnum Shaheen8, Alia Anwar2, Muhammad Shafiq Ahmad2, Urooj Mubashar9. 1. Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan. ashfaq.iags@pu.edu.pk. 2. Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan. 3. Department of Biosciences, COMSATS University Islamabad (CUI), Park Road, 45550, Islamabad, Pakistan. 4. Department of Entomology Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan. 5. Department of Biosciences, COMSAT University, Islamabad, Pakistan. 6. Department of Zoology, Government College University Faisalabad, Faisalabad, Pakistan. 7. Department of Plant Breeding and Genetics, Bahuddin Zakaria University Bahudar Campus Layyah, Bahudar, Pakistan. 8. Department of Botany, Lahore College for Women University, Lahore, Pakistan. 9. Government Training Education Academy, Gujranwala, Pakistan.
Abstract
BACKGROUND: Rice (Oryza sativa L.) is one of the staple foods worldwide. To feed the growing population, the improvement of rice cultivars is important. To make the improvement in the rice breeding program, it is imperative to understand the similarities and differences of the existing rice accessions to find out the genetic diversity. Previous studies demonstrated the existence of abundant elite genes in rice landraces. A genome-wide association study (GWAS) was performed for yield and yield related traits to find the genetic diversity. DESIGN: Experimental study. METHODS AND RESULTS: A total of 204 SSRs markers were used among 17 SSRs found to be located on each chromosome in the rice genome. The diversity was analyzed using different genetic characters i.e., the total number of alleles (TNA), polymorphic information content (PIC), and gene diversity by Power markers, and the values for each genetic character per marker ranged from 2 to 9, 0.332 to 0.887 and 0.423 to 0.900 respectively across the whole genome. The results of population structure identified four main groups. MTA identified several markers associated with many agronomically important traits. These results will be very useful for the selection of potential parents, recombinants, and MTAs that govern the improvements and developments of new high yielding rice varieties. CONCLUSIONS: Analysis of diversity in germplasm is important for the improvement of cultivars in the breeding program. In the present study, the diversity was analyzed with different methods and found that enormous diversity was present in the studied rice germplasm. The structure analysis found the presence of 4 genetic groups in the existing germplasm. A total of 129 marker-trait associations (MTAs) have been found in this study.
BACKGROUND: Rice (Oryza sativa L.) is one of the staple foods worldwide. To feed the growing population, the improvement of rice cultivars is important. To make the improvement in the rice breeding program, it is imperative to understand the similarities and differences of the existing rice accessions to find out the genetic diversity. Previous studies demonstrated the existence of abundant elite genes in rice landraces. A genome-wide association study (GWAS) was performed for yield and yield related traits to find the genetic diversity. DESIGN: Experimental study. METHODS AND RESULTS: A total of 204 SSRs markers were used among 17 SSRs found to be located on each chromosome in the rice genome. The diversity was analyzed using different genetic characters i.e., the total number of alleles (TNA), polymorphic information content (PIC), and gene diversity by Power markers, and the values for each genetic character per marker ranged from 2 to 9, 0.332 to 0.887 and 0.423 to 0.900 respectively across the whole genome. The results of population structure identified four main groups. MTA identified several markers associated with many agronomically important traits. These results will be very useful for the selection of potential parents, recombinants, and MTAs that govern the improvements and developments of new high yielding rice varieties. CONCLUSIONS: Analysis of diversity in germplasm is important for the improvement of cultivars in the breeding program. In the present study, the diversity was analyzed with different methods and found that enormous diversity was present in the studied rice germplasm. The structure analysis found the presence of 4 genetic groups in the existing germplasm. A total of 129 marker-trait associations (MTAs) have been found in this study.
Authors: Arnold T W Kraakman; Rients E Niks; Petra M M M Van den Berg; Piet Stam; Fred A Van Eeuwijk Journal: Genetics Date: 2004-09 Impact factor: 4.562
Authors: Jianming Yu; Gael Pressoir; William H Briggs; Irie Vroh Bi; Masanori Yamasaki; John F Doebley; Michael D McMullen; Brandon S Gaut; Dahlia M Nielsen; James B Holland; Stephen Kresovich; Edward S Buckler Journal: Nat Genet Date: 2005-12-25 Impact factor: 38.330
Authors: Alkes L Price; Nick J Patterson; Robert M Plenge; Michael E Weinblatt; Nancy A Shadick; David Reich Journal: Nat Genet Date: 2006-07-23 Impact factor: 38.330
Authors: Susan R McCouch; Leonid Teytelman; Yunbi Xu; Katarzyna B Lobos; Karen Clare; Mark Walton; Binying Fu; Reycel Maghirang; Zhikang Li; Yongzhong Xing; Qifa Zhang; Izumi Kono; Masahiro Yano; Robert Fjellstrom; Genevieve DeClerck; David Schneider; Samuel Cartinhour; Doreen Ware; Lincoln Stein Journal: DNA Res Date: 2002-12-31 Impact factor: 4.458