Genetic dissection of rice appearance quality and cooked rice elongation by genome-wide association study

Qiu, Xianjin; Yang, Jing; Zhang, Fan; Niu, Yanan; Zhao, Xiu-qing; Shen, Congcong; Chen, Kai; Teng, Sheng; Xu, Jianlong

doi:10.1016/j.cj.2020.12.010

Cited by 19 publications

(20 citation statements)

References 40 publications

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“…GWAS was conducted to identify QTL for Se, Cd and As concentrations, and ratio of Se, Cd and As concentrations of treatment to normal conditions in brown and milled rice using 405,150 high quality SNPs and trait values of the 307 accessions. The SVS software package v8.4.0 was used for association analysis ( Qiu X. et al, 2021 ). The EMMAX (Efficient Mix-Model Association eXpedited) implementation of the single-locus mixed linear model was fitted to the marker dataset ( Vilhjálmsson and Nordborg, 2013 ).…”

Section: Methodsmentioning

confidence: 99%

Distribution characteristics of selenium, cadmium and arsenic in rice grains and their genetic dissection by genome-wide association study

et al. 2022

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High selenium (Se) and low cadmium (Cd) and arsenic (As) contents in rice grains were good for human health. The genetic basis and relationship of Se, Cd and As concentrations in rice grains are still largely unknown. In the present study, large variations were observed in Se, Cd and As concentrations in brown and milled rice in normal and Se treatment conditions in 307 rice accessions from 3K Rice Genomes Project. Se fertilizer treatment greatly increased Se concentrations but had no obvious changes in concentrations of Cd and As both in brown and milled rice. Total of 237 QTL were identified for Se, Cd and As concentrations in brown and milled rice in normal and Se treatment conditions as well as ratio of concentrations under Se treatment to normal conditions. Only 19 QTL (13.4%) were mapped for concentrations of Se and Cd, Se and As, and Se, Cd and As in the same or adjacent regions, indicating that most Se concentration QTL are independent of Cd and As concentration QTL. Forty-three favorable alleles were identified for 40 candidate genes by gene-based association study and haplotype analysis in 14 important QTL regions. Se-enriched rice variety will be developed by pyramiding favorable alleles at different Se QTL and excluding undesirable alleles at Cd and As QTL, or combining favorable alleles at Se QTL with the alleles at Se-sensitive QTL by marker-assisted selection.

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Section: Methodsmentioning

confidence: 99%

Distribution characteristics of selenium, cadmium and arsenic in rice grains and their genetic dissection by genome-wide association study

et al. 2022

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“…This quality denotes the grain shapes like the length, width, and their ratio, and grain chalkiness [16]. Chalkiness could be classified into white belly, white back, and white core according to its location in the endosperm.…”

Section: Grain Appearance Quality: Color Shape and Sizementioning

confidence: 99%

Genomic-Assisted Breeding Tools for Grain and Nutritional Quality Improvement in Rice

Patra

Majhi

Tripathy

et al. 2022

IJECC

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More than half of the world’s population consumes rice as a staple food in their diet. Rice grain quality is receiving attention from both consumers and producers as living standards in rice-consuming regions has improved and this emerged as a critical rice breeding target. Grain quality traits have a strong influence on the market value of rice and the adoption of new varieties by farmers. Consumer preferences for specific nutritional, physical, eating, and cooking characteristics are at the root of these. Uniform grain width, length, colour (translucence or whiteness), and chalkiness are all desirable physical properties. Cooking and eating (organoleptic) characteristics such as; cooking time (gelatinization temperature and viscosity), the ability of rice to remain soft after cooking (gel consistency), and textural properties of cooked rice (amylose content and aroma) are also very important. Plant breeders are always working hard to meet these demands by developing new rice varieties. The genomics era provides many opportunities to assist breeders in addressing these challenges. While not complete, our understanding of the genetic basis underlying many grain quality traits is expanding. There have been reports of quantitative trait loci (QTL) controlling grain appearance, chalkiness, protein content, and grain length. Genomic-assisted Breeding techniques such as marker-assisted selection, QTL mapping, genome editing, genome wide association studies, and genetic engineering can provide further a better understanding of the genetic basis and thus help to improve rice grain nutritional quality traits.

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“…In premium quality rice such as Basmati, where quality enjoys equal, sometimes even more weightage than grain yield, traits such as kernel length before cooking, kernel length after cooking, and length-breadth ratio are considered major physical quality traits that largely determine consumer preference. Several studies have reported the allelic variations for kernel length before cooking, and the length-breadth ratio in rice through GWAS (Ponce et al, 2020;Qiu et al, 2021). Employing GWAS, Misra et al (2017) identified MTAs associated with cooked and raw grain length, width and shape.…”

Section: Introductionmentioning

confidence: 99%

“…Genome-wide association study (GWAS) is a very popular quantitative genomics tool, which has gained prominence in mapping quantitative traits with the advent of high-density genotyping platforms, like SNP arrays. GWAS has played a pivotal role in identifying many important genes which govern various complex agronomic traits such as flowering time, plant height and panicle length in rice ( Begum et al., 2015 ; Yano et al., 2016 ; Reig-Valiente et al., 2018 ; Zhang et al., 2019 ; Zhou and Huang, 2019 ; Verma et al., 2021 ), particularly using collections of unrelated diverse germplasm ( Huang et al., 2012 ; Qiu et al., 2021 ; Ravikiran et al., 2022 ). Although GWAS is helpful in mining novel alleles for complex traits, it requires further validation in breeding populations for its usefulness in marker-assisted breeding ( Begum et al., 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study reveals novel genomic regions governing agronomic and grain quality traits and superior allelic combinations for Basmati rice improvement

et al. 2022

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BackgroundBasmati is a speciality segment in the rice genepool characterised by explicit grain quality. For the want of suitable populations, genome-wide association study (GWAS) in Basmati rice has not been attempted.MaterialsTo address this gap, we have performed a GWAS on a panel of 172 elite Basmati multiparent population comprising of potential restorers and maintainers. Phenotypic data was generated for various agronomic and grain quality traits across seven different environments during two consecutive crop seasons. Based on the observed phenotypic variation, three agronomic traits namely, days to fifty per cent flowering, plant height and panicle length, and three grain quality traits namely, kernel length before cooking, length breadth ratio and kernel length after cooking were subjected to GWAS. Genotyped with 80K SNP array, the population was subjected to principal component analysis to stratify the underlying substructure and subjected to the association analysis using Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model.ResultsWe identified 32 unique MTAs including 11 robust MTAs for the agronomic traits and 25 unique MTAs including two robust MTAs for the grain quality traits. Six out of 13 robust MTAs were novel. By genome annotation, six candidate genes associated with the robust MTAs were identified. Further analysis of the allelic combinations of the robust MTAs enabled the identification of superior allelic combinations in the population. This information was utilized in selecting 77 elite Basmati rice genotypes from the panel.ConclusionThis is the first ever GWAS study in Basmati rice which could generate valuable information usable for further breeding through marker assisted selection, including enhancing of heterosis.

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Genetic dissection of rice appearance quality and cooked rice elongation by genome-wide association study

Cited by 19 publications

References 40 publications

Distribution characteristics of selenium, cadmium and arsenic in rice grains and their genetic dissection by genome-wide association study

Distribution characteristics of selenium, cadmium and arsenic in rice grains and their genetic dissection by genome-wide association study

Genomic-Assisted Breeding Tools for Grain and Nutritional Quality Improvement in Rice

Genome-wide association study reveals novel genomic regions governing agronomic and grain quality traits and superior allelic combinations for Basmati rice improvement

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