Identification of Promising RILs for High Grain Zinc Through Genotype × Environment Analysis and Stable Grain Zinc QTL Using SSRs and SNPs in Rice (Oryza sativa L.)

Abstract

Polished rice is one of the commonly consumed staple foods across the world. However, it contains limited nutrients especially iron (Fe) and zinc (Zn). To identify promising recombinant inbred lines (RILs) for grain Zn and single plant yield, 190 RILs developed from PR116 and Ranbir Basmati were evaluated in two environments (E1 and E2). A subset of 44 contrasting RILs for grain Zn was screened in another two environments (E3 and E4). Phenotypic data was collected for 10 traits, viz., days to 50% flowering, plant height, panicle length, number of tillers, single plant yield (SPY), test weight, Fe and Zn in brown (IBR, ZBR), and polished rice (IPR, ZPR). Stepwise regression analysis of trait data in 190 RILs and a subset of 44 RILs revealed the interdependence of ZPR, ZBR, IPR, and IBR and the negative association of grain Zn with single plant yield. Based on the additive main effect and multiplicative interaction (AMMI) and genotype and genotype × environment interaction (GGE) analyses of the subset of 44 RILs across four environments (E1–E4), six promising RILs were identified for ZPR with >28 ppm. Mapping of 190 RILs with 102 simple sequence repeats (SSRs) resulted in 13 QTLs for best linear unbiased estimates (BLUEs) of traits including advantage over check (AOC). Using genotype-based sequencing (GBS), the subset of 44 RILs was mapped with 1035 single-nucleotide polymorphisms (SNPs) and 21 QTLs were identified. More than 100 epistatic interactions were observed. A major QTL qZPR.1.1 (PV 37.84%) and another QTL qZPR.11.1 (PV 15.47%) were identified for grain Zn in polished rice. A common major QTL (qZBR.2.1 and qZPR.2.1) was also identified on chromosome 2 for grain Zn content across SSR and SNP maps. Two potential candidate genes related to transporters were identified based on network analyses in the genomic regions of QTL < 3 Mb. The RILs identified for grain Zn and SPY were nominated for national evaluation as under rice biofortification, and two QTLs identified based on BLUEs could be used in the rice biofortification breeding programs.

GGE Biplot Analysis for Stability in Diverse Maturity Groups of Rice (Oryza sativa L.) Advanced Lines

“…Rice has been widely consumed as an essential food for human beings and grown around the world. Over half of the world's population constantly include rice in their diet (Rao et al, 2016;Nili et al, 2017;Sharifi et al, 2017;Poli et al, 2018;Suman et al, 2021) and Asian countries produce nearly 80% of rice in the world. Among rice growing countries in the world, India has the largest area under rice crop of about 44.1 million hectares with a production of 165.3 million tons; however, its productivity per unit area is low i.e 3.78 t ha -1 (Kesh et al, 2021).…”

Zinc in plants: Integrating homeostasis and biofortification

“…Znrelated chromosome regions found in elite wheat cultivars can be utilized to inform gene transfer studies from Znaccumulating wild species, as carried out between the high-Zn and -Fe Aegilops species and bread wheat (Sharma et al, 2018). Improved rice genome sequences allowed the exploitation of markers, such as simple sequence repeats and single-nucleotide polymorphisms, to identify QTLs for grain Zn and yield in recombinant inbred lines, which led to the establishment of stable lines with desired traits (Suman et al, 2021). As such, QTL analysis of rice doubled haploid lines identified candidate genes associated with both agronomic traits, yield and high concentrations of Zn in grains, for example, genes encoding transporters such as OsZIP6, but also transcription factors (e.g., OsGATA8) and GTPases involved in endosperm protein deposition (e.g., OsSar1) (Calayugan et al, 2020).…”

Biofortification of iron and zinc in rice and wheat

“…More recently, Liu et al (2021a) reported that a grain zinc content ranging from 38.22 to 101.38 µg/g in a Chinese wheat mini core collection contained 246 germplasms. However, there have been few large‐scale analyses of endosperm iron and zinc contents in rice and wheat (Zhang et al, 2018a; Suman et al, 2021). In a set of 698 rice germplasms, the concentrations of iron and zinc in the polished rice ranged from 0.9 to 9.1 µg/g and 5.8 to 29.6 µg/g, respectively (Zhang et al, 2018a).…”

“…An association analysis of zinc content of 40 genotypes in three environments showed that single nucleotide polymorphisms located in three putative candidate genes on chromosomes 3 and 7 are associated with high zinc content in polished rice (Babu et al, 2020). An analysis of zinc contents in brown and polished rice from 190 recombinant inbred lines (RILs) in four environments identified two major QTL ( qZPR.1.1 and qZPR.11.1 ) for grain zinc content in polished rice on chromosomes 1 and 11, and a common major QTL ( qZBR.2.1 and qZPR.2.1 ) for zinc content in brown and polished rice was identified on chromosome 2 (Suman et al, 2021).…”