Dataset Information

Identification of Genomic Regions Associated with High Grain Zn Content in Polished Rice Using Genotyping-by-Sequencing (GBS).

ABSTRACT: Globally, micronutrient (iron and zinc) enriched rice has been a sustainable and cost-effective solution to overcome malnutrition or hidden hunger. Understanding the genetic basis and identifying the genomic regions for grain zinc (Zn) across diverse genetic backgrounds is an important step to develop biofortified rice varieties. In this case, an RIL population (306 RILs) obtained from a cross between the high-yielding rice variety MTU1010 and the high-zinc rice variety Ranbir Basmati was utilized to pinpoint the genomic region(s) and QTL(s) responsible for grain zinc (Zn) content. A total of 2746 SNP markers spanning a genetic distance of 2445 cM were employed for quantitative trait loci (QTL) analysis, which resulted in the identification of 47 QTLs for mineral (Zn and Fe) and agronomic traits with 3.5-36.0% phenotypic variance explained (PVE) over the seasons. On Chr02, consistent QTLs for grain Zn polished (qZnPR.2.1) and Zn brown (qZnBR.2.2) were identified. On Chr09, two additional reliable QTLs for grain Zn brown (qZnBR.9.1 and qZnBR.9.2) were identified. The major-effect QTLs identified in this study were associated with few key genes related to Zn and Fe transporter activity. The genomic regions, candidate genes, and molecular markers associated with these major QTLs will be useful for genomic-assisted breeding for developing Zn-biofortified varieties.

SUBMITTER: Uttam GA

PROVIDER: S-EPMC9824299 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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Identification of Genomic Regions Associated with High Grain Zn Content in Polished Rice Using Genotyping-by-Sequencing (GBS).

Uttam Goparaju Anurag GA Suman Karre K Jaldhani Veerendra V Babu Pulagam Madhu PM Rao Durbha Sanjeeva DS Sundaram Raman Meenakshi RM Neeraja Chirravuri Naga CN

Plants (Basel, Switzerland) 20221228 1

Globally, micronutrient (iron and zinc) enriched rice has been a sustainable and cost-effective solution to overcome malnutrition or hidden hunger. Understanding the genetic basis and identifying the genomic regions for grain zinc (Zn) across diverse genetic backgrounds is an important step to develop biofortified rice varieties. In this case, an RIL population (306 RILs) obtained from a cross between the high-yielding rice variety MTU1010 and the high-zinc rice variety Ranbir Basmati was utiliz ...[more]

PMID: 36616273

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Project description:Zinc is an essential minor element for rice growth and human health, which can also change the structure of the microorganisms. However, it remains unclear for the effects of zinc fertilizer on microbiome function in agricultural soils and crops. To solve this research gap, we investigated the relationship between improving rice (Oryza sativa L.) yield, Zn concentration, soil microbial community diversity, and function by the application of Zn fertilizer. The field trials included three rice varieties (Huanghuazhan, Nanjing9108, and Nuodao-9925) and two soil Zn levels (0 and 30 kg ha-1) in Jiangsu province, China. As a test, we studied the variety of soil bacterial composition, diversity, and function using 16S rRNA gene sequencing. The results showed that soil Zn application reduced the diversity of microbial community, but the bacterial network was more closely linked, and the metabolic function of bacterial community was improved, which increased the grain yield (17.34-19.52%) and enriched the Zn content of polished rice (1.40-20.05%). Specifically, redundancy analysis (RDA) and Mantel's test results revealed soil total nitrogen (TN) was the primary driver that led to a community shift in the rice rhizosphere bacterial community, and soil organic carbon (SOC) was considered to have a strong influence on dominant phyla. Furthermore, network analysis indicated the most critical bacterial taxa were identified as Actinobacteria, Bacteroidetes, Proteobacteria, and Chloroflexi based on their topological roles of microorganisms. KEGG metabolic pathway prediction demonstrated that soil Zn application significantly (p < 0.05) improved lipid metabolism, amino acid metabolism, carbohydrate metabolism, and xenobiotic biodegradation. Overall, their positive effects were different among rice varieties, of which Nanjing-9108 (NJ9108) performed better. This study opens new avenues to deeply understand the plant and soil-microbe interactions by the application of fertilizer and further navigates the development of Zn-rich rice cultivation strategies.

Project description: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 (rMQTL7.1) 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.

Dataset Information

Identification of Genomic Regions Associated with High Grain Zn Content in Polished Rice Using Genotyping-by-Sequencing (GBS).

Publications

Identification of Genomic Regions Associated with High Grain Zn Content in Polished Rice Using Genotyping-by-Sequencing (GBS).

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