Stable SNP Allele Associations With High Grain Zinc Content in Polished Rice (Oryza sativa L.) Identified Based on ddRAD Sequencing

Abstract

Polished rice is widely consumed staple food across the globe, however, it contains limited nutrients especially iron (Fe) and zinc (Zn). To identify promising genotypes for grain Zn, a total of 40 genotypes consisting 20 rice landraces, and 20 released high yielding rice varieties were evaluated in three environments (wet seasons 2014, 2015 and 2016) for nine traits including days to 50% flowering (DFF), plant height (PH), panicle length (PL), total number of tillers (TNT), single plant yield (SPY), Fe and Zn in brown (IBR, ZBR) and polished rice (IPR, ZPR). Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) analyses identified genotypes G22 (Edavankudi Pokkali), G17 (Taraori Basmati), G27 (Chittimuthyalu) and G26 (Kalanamak) stable for ZPR and G8 (Savitri) stable for SPY across three environments. Significant negative correlation between yield and grain Zn was reaffirmed. Regression analysis indicated the contribution of traits toward ZPR and SPY and also desirable level of grain Zn in brown rice. A total of 39,137 polymorphic single nucleotide polymorphisms (SNPs) were obtained through double digest restriction site associated DNA (dd-RAD) sequencing of 40 genotypes. Association analyses with nine phenotypic traits revealed 188 stable SNPs with six traits across three environments. ZPR was associated with SNPs located in three putative candidate genes (LOC_Os03g47980, LOC_Os07g47950 and LOC_Os07g48050) on chromosomes 3 and 7. The genomic region of chromosome 7 co localized with reported genomic regions (rMQTL 7. 1) and OsNAS3 candidate gene. SPY was found to be associated with 12 stable SNPs located in 11 putative candidate genes on chromosome 1, 6, and 12. Characterization of rice landraces and varieties in terms of stability for their grain Zn and yield identified promising donors and recipients along with genomic regions in the present study to be deployed rice Zn biofortification breeding program.

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.)

“…Through the Which Won Where/What plot, common winners could not be found across four environments for the 10 traits of study which could be due to the variability of performance of the RILs across wet and dry seasons. For rice grain Zn and Fe, stability and G × E analyses are generally used for identification of stable donors ( Suwarto and Nasrullah, 2011 ; Ajmera et al, 2017 ; Babu et al, 2020 ; Naik et al, 2020 ). Considering the wide variability observed for the breeding lines with high grain Zn and Fe, stability and G × E analyses are being recently applied for selecting promising RILs in cereals.…”

“…A modified GBS technique is based on two restriction enzymes comprising rare cutting and frequently cutting as double-digest restriction-site-associated DNA sequencing (ddRAD-seq) for enhancing the stability of selected genomic regions ( Peterson et al, 2012 ). GBS is being deployed in many crop genomics studies ( Gali et al, 2019 ; Sudan et al, 2019 ; Dissanayaka et al, 2020 ) and also in rice ( De Leon et al, 2016 ; Furuta et al, 2017 ; Bhatia et al, 2018 ; Yadav et al, 2019 ; Babu et al, 2020 ).…”

Identifying genes associated with abiotic stress tolerance suitable for CRISPR/Cas9 editing in upland rice cultivars adapted to acid soils

“…On the other hand, the molar ratios of phytate:Zn were much lower (Figure S5 ). Typical Zn levels in polished rice are low (8–12 ppm), but there is a wide genetic variability in brown (7.3 to 52.7 ppm) and polished (8 to 38 ppm) rice (Babu et al, 2020 ). The primary inhibitor of Zn is phytate (Lönnerdal, 2000 ) and more Zn, as observed in the mutants and Colombian genotypes of this study (Figure 5f ), usually means more absorbed Zn.…”

Biofortification of iron and zinc in rice and wheat

“…Importantly, 12 of these were the most prominent stable QTL across different seasons, locations, environments, and populations (Swamy et al, 2021). 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).…”