Association Analysis of Markers Derived from Starch Biosynthesis Related Genes with Starch Physicochemical Properties in the USDA Rice Mini-Core Collection

Li, Kehu; Bao, Jinsong; Corke, Harold; Sun, Mei

doi:10.3389/fpls.2017.00424

Cited by 17 publications

(19 citation statements)

References 69 publications

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“…These efforts have been made possible by the advent of high-throughput genotyping and bioinformatics capacities. For instance, Yang et al (2014) and Li, Bao, Corke, & Sun, 2017 have used the Wx and SSIIa SNPs as covariates in an association mapping approach that takes the gross-level population structure and kinship (Q + K) into account. Results from their studies indicate that variability within the same GT class is associated with several SSR markers and other starch synthesis-related genes such as Wx , SSIIc , SBE1 , SSIIb , and ISA3 .…”

Section: Rice Quality As Predicted By Genesmentioning

confidence: 99%

Rice quality: How is it defined by consumers, industry, food scientists, and geneticists?

Custodio

Cuevas

Ynion

et al. 2019

Trends in Food Science & Technology

211

141

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BackgroundQuality is a powerful engine in rice value chain upgrading. However, there is no consensus on how “rice quality” should be defined and measured in the rice sector.Scope and approachWe adopt a Lancasterian definition of rice quality as a bundle of intrinsic and extrinsic attributes. We then review how rice quality is (i) perceived and defined by consumers and industry stakeholders in rice value chains in Southeast and South Asia; (ii) measured and defined by food technologists; and (iii) predicted through genetics.Key findings and conclusionsConsumers are heterogeneous with respect to their perceived differentiation of rice quality among regions, countries, cities, and urbanization levels. Premium quality is defined by nutritional benefits, softness and aroma in Southeast Asia, and by the physical appearance of the grains (uniformity, whiteness, slenderness), satiety, and aroma in South Asia. These trends are found to be consistent with industry perceptions and have important implications for regional and national breeding programs in terms of tailoring germplasm to regions and rice varieties to specific local market segments. Because rice is traded internationally, there is a need to standardize definitions of rice quality. However, food technologists have not reached unanimity on quality classes and measurement; routine indicators need to be complemented by descriptive profiles elicited through sensory evaluation panels. Finally, because rice quality is controlled by multiple interacting genes expressed through environmental conditions, predicting grain quality requires associating genetic information with grain quality phenotypes in different environments.

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Section: Rice Quality As Predicted By Genesmentioning

confidence: 99%

Rice quality: How is it defined by consumers, industry, food scientists, and geneticists?

Custodio

Cuevas

Ynion

et al. 2019

Trends in Food Science & Technology

211

141

View full text Add to dashboard Cite

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“… 27) 28) In addition, (CT)n repeats located in the untranslated region of exon 1, as well as C/T SNP (415 th residue Pro/Ser) in exon 10, are found in the Wx gene of various non-glutinous rice cultivars. 38) 39) 40) …”

Section: Introductionmentioning

confidence: 99%

Three Major Nucleotide Polymorphisms in the <i>Waxy</i> Gene Correlated with the Amounts of Extra-long Chains of Amylopectin in Rice Cultivars with S or L-type Amylopectin

et al. 2019

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Extra-long chains (ELC) of amylopectin in rice endosperm are synthesized by granule-bound starch synthase I encoded by the Waxy (Wx) gene, which primarily synthesizes amylose. Previous studies showed that single nucleotide polymorphisms (SNP) in intron 1 and exon 6 of the Wx gene influences ELC amount. However, whether these SNPs are conserved among rice cultivars and if any other SNPs are present in the Wx gene remained unknown. Here, we sequenced the Wx gene from 17 rice cultivars with S or L-type amylopectin, including those with known ELC content and those originating in China with unique starch properties, as well as typical japonica and indica cultivars. In addition to the two SNPs described above, an additional SNP correlating with ELC content was found in exon 10. Low ELC cultivars (<3.0 %) had thymine at the splicing donor site of intron 1, Tyr224 in exon 6, and Pro415 in exon 10. Cultivars with moderate ELC content (4.1-6.9 %) had guanine at the splicing donor site of intron 1, Ser224 in exon 6, and Pro415 in exon 10. Cultivars with high ELC content (7.7-13.9 %) had guanine at the splicing donor site of intron 1, Tyr224 in exon 6, and Ser415 in exon 10. The chain length distribution pattern of amylopectin was correlated with the amounts of SSIIa found in starch granules and gelatinization temperature, but not with ELC content. The combinations of SNPs in the Wx gene found in this study may provide useful information for screening specific cultivars with different ELC content.

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“…The United States Department of Agriculture (USDA) rice mini-core collection (URMC) is a subset of 217 accessions containing similar phenotypic, genotypic, and geographical diversity as present in the USDA rice core collection of 1794 accessions representing rice-growing countries around the globe [35,36]. The URMC has been successfully used by rice researchers for identifying sources of germplasm and novel QTLs for several important traits such as: grain yield [35,37,38], grain yield components and harvest index [39], silica content in hulls [40], grain quality [23], grain protein content [41], grain starch quality [42], sheath blight resistance [43,44], and cold tolerance at seed germination and the seedling stage [45]. These evaluations have provided insights into the beneficial phenotypic and genotypic diversity available in the URMC for rice breeding programs.…”

Section: Introductionmentioning

confidence: 99%

Identification of Superior Alleles for Seedling Stage Salt Tolerance in the USDA Rice Mini-Core Collection

Rohila

Edwards

Tran³

et al. 2019

Plants

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Salt stress is a major constraint to rice acreage and production worldwide. The purpose of this study was to evaluate the natural genetic variation available in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) for early vigor traits under salt stress and identify quantitative trait loci (QTLs) for seedling-stage salt tolerance via a genome-wide association study (GWAS). Using a hydroponic system, the seedlings of 162 accessions were subjected to electrical conductivity (EC) 6.0 dS m−1 salt stress at the three-to-four leaf stage. After completion of the study, 59.4% of the accessions were identified as sensitive, 23.9% were identified as moderately tolerant, and 16.7% were identified as highly tolerant. Pokkali was the most tolerant variety, while Nerica-6 was the most sensitive. Adapting standard International Rice Research Institute (IRRI) protocols, eight variables associated with salt tolerance were determined. The GWAS of the URMC, using over three million single-nucleotide polymorphisms (SNPs), identified nine genomic regions associated with salt tolerance that were mapped to five different chromosomes. Of these, none were in the known Saltol QTL region, suggesting different probable genes and mechanisms responsible for salt tolerance in the URMC. The study uncovered genetic loci that explained a large portion of the variation in salt tolerance at the seedling stage. Fourteen highly salt-tolerant accessions, six novel loci, and 16 candidate genes in their vicinity were identified that may be useful in breeding for salt stress tolerance. Identified QTLs can be targeted for fine mapping, candidate gene verification, and marker-assisted breeding in future studies.

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Association Analysis of Markers Derived from Starch Biosynthesis Related Genes with Starch Physicochemical Properties in the USDA Rice Mini-Core Collection

Cited by 17 publications

References 69 publications

Rice quality: How is it defined by consumers, industry, food scientists, and geneticists?

Rice quality: How is it defined by consumers, industry, food scientists, and geneticists?

Three Major Nucleotide Polymorphisms in the <i>Waxy</i> Gene Correlated with the Amounts of Extra-long Chains of Amylopectin in Rice Cultivars with S or L-type Amylopectin

Identification of Superior Alleles for Seedling Stage Salt Tolerance in the USDA Rice Mini-Core Collection

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