Philippine E-Journals

Genotyping by Sequencing Based QTL Mapping for Yield, Grain Zinc and Iron Concentration of Rice (Oryza sativa L.)

Mark Ian C. Calaguyan | Gwen Iris Descalsota-empleo | Chau Thanh Nha | Alvin D. Palanog | Amery Amparado | Mary Ann Inabangan-asilo | Teresita H. Borromeo | Jose E. Hernandez | B.p Mallikarjuna Swamy

 

Abstract:

Rice (Oryza sativa L.) is one of the most important food crops and serves as the principal source of calories for more than half of the world's population. Development of high-yielding rice varieties with improve grain Zn and Fe concentration is essential to help solve micronutrient malnutrition. This study was conducted at the ZES, Strategic Innovation Platform of the International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines. Genotyping-by-sequencing (GBS) based high-density linkage map of rice was developed using two recombinant inbred lines (RILs) mapping populations namely IR95040/Kaliboro (2018 SNPs covering 1232.22 cM) and IR95097/Kaliboro (2213 SNPs covering 1071.53 cM) with an average marker density of 0.61 cM and 0.48 cM, respectively. The parental lines IR95040 and IR95097 have irrigated lowland breeding lines while Kaliboro is an Aus-type rice variety known to have high grain Zn and Fe concentrations. RILs were grown in an alpha lattice design with two replications each during the 2017 dry and wet seasons, and 2018 dry seasons. In total, five QTL for YLD were identified on chromosomes 4, 6, and 7, with phenotypic variance, explained (PVE) ranged from 7.07-14.86%. For Fe, three QTL (qFe4.1, qFe6.1, and qFe6.2) were identified on chromosomes 4 and 6. The favorable donor allele Kaliboro has contributed to the high Fe concentration in qFe4.1 and qFe6.1. A total of 12 QTL associated with Zn were identified on chromosomes 3, 4, 5, 6, 7, 8, 10, and 12, which accounted for 5.17-18.33% of PVE. Four QTL were consistently detected on chromosomes 3, 7, and 10 in IR95040/Kaliboro and on chromosome 4 in IR95040/Kaliboro viz. qZn3.1, qZn7.3, qZn10.1, and qZn4.1. Validation of the genomic regions reported in this study will help accelerate the development of SNP chips for breeding healthier rice varieties and will be beneficial in the rapid development and deployment of biofortified rice varieties.