Genome-wide association mapping revealed numerous novel genomic loci for grain nutritional and yield-related traits in rice (Oryza sativa L.) landraces

Parmeshwar K Sahu; Suvendu Mondal; Richa Sao; Gautam Vishwakarma; Vikash Kumar; B K Das; Deepak Sharma

doi:10.1007/s13205-020-02467-z

Genome-wide association mapping revealed numerous novel genomic loci for grain nutritional and yield-related traits in rice (Oryza sativa L.) landraces

3 Biotech. 2020 Nov;10(11):487. doi: 10.1007/s13205-020-02467-z. Epub 2020 Oct 24.

Authors

Parmeshwar K Sahu¹, Suvendu Mondal^{2

3}, Richa Sao¹, Gautam Vishwakarma^{2

3}, Vikash Kumar^{2

3}, B K Das^{2

3}, Deepak Sharma¹

Affiliations

¹ Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh 492012 India.
² Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India.
³ Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India.

Abstract

A core set of 190 rice landraces were used to decipher the genetic structure and to discover the chromosomal regions containing QTLs, affecting the grain micro-nutrients, fatty acids, and yield-related traits by using 148 molecular markers in this study. Landraces were categorized into three sub-groups based on population stratification study and followed by neighbor-joining tree and principal component analysis. Analysis of variance revealed abundant variations among the landraces for studied traits with less influence of environmental factors. Genome Wide Association Studies (GWAS) revealed 22 significant and consistent QTLs through marker trait association (MTAs) for 12 traits based on 2 years and pooled analysis. Out of 22 QTLs, three have been reported earlier while 19 QTLs are novel. Interestingly, 13 QTLs out of 22 were explained more than 10% phenotypic variance. Association of RM1148 and RM205 with Days to 50% flowering was comparable with flowering control genes Ghd8/qDTH8 and qDTH9, respectively. Similarly, Zn content was associated with RM44, which is situated within the QTL qZn8-1. Moreover, significant association of RM25 with oleic acid content was closely positioned with QTL qOle8. Association of RM7434 with grain yield/plant; RM184 with spikelet fertility %; R3M10, R9M42 with hundred seed weight; RM536, RM17467, RM484, RM26063 with Fe content; RM44, RM6839 with Zn content are the major outcomes of this study. In addition, association of R11M23 with days to 50% flowering, panicle length and total spikelets per panicle are explained the possible occurrence of pleiotropism among these traits. Prominent rice landraces viz., Anjani (early maturity); Sihar (extra dwarf); Gangabaru (highest grain yield/plant); Karhani (highest iron content); Byalo-2 (highest zinc content) and Kadamphool (highest oleic acid) were identified through this study. The present study will open many avenues towards utilization of these QTLs and superior landraces in rice breeding for developing nutrition-rich high yielding varieties.

Keywords: Association mapping; Fatty acids; Micronutrients; Qtls; Rice landraces.