Increasing iron and zinc in rice grains using deep water rices and wild species - identifying genomic segments and candidate genes

Abstract

Large genetic variation exists for grain iron and zinc in rice germplasm including wild species and deep water rices. Conventional breeding is an easy and acceptable approach to biofortify rice. Analysis of 126 rice accessions using atomic absorption spectrophotometry showed that Fe concentration in brown rice ranged from 6 ppm in Athira to 72 ppm in O. nivara and Zn concentration from 27 ppm in Jyothi to 67 ppm in O. rufipogon. Quantitative trait loci (QTL) for high Fe and Zn concentration in grains were mapped from 3 wild progenitors and 2 deep water rices with the aim of gene discovery and also to develop iron/zinc-rich lines of two widely grown, popular rice varieties Swarna (MTU7029) and Samba Mahsuri (BPT5204) through conventional breeding approaches. Three advanced backcross mapping populations were developed using 3 wild accessions: Swarna x O.nivara IRGC81832, Swarna x O.nivara IRGC81848 and Samba Mahsuri x O.rufipogon WR119. In addition, F7 recombinant inbred lines (RILs) were developed from two crosses: Madhukar x Swarna and Jalmagna x Swarna. Madhukar and Jalmagna are deep-water rice varieties with high grain iron and zinc. Overall, Fe concentration ranged from 0.2 to 224 ppm and Zn concentration from 0.4 to 104 ppm in the 5 mapping populations. QTLs for Fe and Zn concentration in polished rice were mapped from two Swarna x O. nivara BC2F3 mapping populations using accession IRGC81848- 227 families, 100 SSR markers and accession IRGC81832- 245 families, 75 SSR markers. qFe2.1, qFe3.1, qFe8.1 and qFe8.2 coincided in the two populations. QTLs for Fe and Zn concentration coincided on chromosomes 2, 3, 8 and 12. Five QTLs for Fe and 3 QTLs for Zn each explained more than 15% phenotypic variance. QTLs were also mapped for Fe and Zn concentration in brown rice from Madhukar x Swarna F7 RILs using 110 SSR markers including 9 gene specific markers. Seven QTLs for Fe and six QTLs for Zn were identified each explaining >30% phenotypic variance. QTLs for Fe and Zn concentration coincided on chromosomes 7 and 12. Madhukar allele increased Fe in qFe7.1 and qFe7.2 and Swarna allele increased Zn in qZn12.1 and qZn12.2. Only two QTL flanking markers RM243 for qFe1.1 and RM517 for qZn3.1 were common in the 3 mapping populations. Genotyping of 2 populations is in progress. Candidate genes OsYSL1, OsNAC, OsYSL16, OsZIP4, OsYSL17 and OsNAAT1 underlie the Fe or Zn QTLs mapped in the Swarna x O.nivara mapping population. Likewise, OsYSL1, OsMTP1, OsNAS1, OsNAS3, OsNRAMP1, heavy metal ion transporter, OsAPRT underly QTLs for Fe and Zn mapped in the Madhukar x Swarna mapping population. In all, 20 elite lines with >80 ppm iron and >50ppm zinc in brown rice were identified from 5 mapping populations. These non-transgenic rice lines with high iron, high zinc or both are a useful resource for functional genomics and biofortification programmes.