Development of low-temperature germinability markers for evaluation of rice (Oryza sativa L.) germplasm

Hyun, Do Yoon; Lee, Gi An; Kang, Man Jung; Burkart‐Waco, Diana; Kim, Sang Ic; Kim, Jae Yoon; Lee, Myung Chul; Gwag, Jae‐Gyun; Kim, Yeon Gyu; Tai, Thomas H.

doi:10.1007/s11032-015-0298-1

Cited by 12 publications

(25 citation statements)

References 39 publications

(71 reference statements)

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“…Therefore, our indica-japonica SNP sets are suitable for genotyping a small number of SNPs and for changing the SNP combination, based on the objective such as target gene screening, genotyping of unfixed early generation populations (e.g., F 2 and BC n F 1 ), and gene/QTL pyramiding by marker-assisted backcrossing (MABC). The Fluidigm platform has been used for target SNP genotyping in various rice genetic studies (Duitama et al 2015;Hyun et al 2015;Lee et al 2017). However, a genome-wide SNP set using Fluidigm has not been reported to date.…”

Section: Discussionmentioning

confidence: 99%

Development and application of indica–japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding

et al. 2020

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Molecular markers are efficient and essential genotyping tools for molecular breeding and genetic analysis of rice. We developed two 96-plex indicajaponica single nucleotide polymorphism (SNP) genotyping sets for genetic analysis and molecular breeding in rice using the Fluidigm platform. Informative SNPs between indica and japonica were selected from SNP data of the Rice Diversity database, HapRice world SNP data of the Q-TARO database, and our 40 rice cultivar resequencing dataset. SNPs in set 1 were evenly distributed across all 12 rice chromosomes at a spacing of 4-5 Mb between adjacent SNPs. SNPs in set 2 mapped to the long genetic intervals in set 1 and included 14 functional or linked SNPs in genes previously cloned and associated with agronomic traits. Additionally, we used the SNP sets developed in this study to perform genetic diversity analysis of various cultivated and wild rice accessions, construction and validation of a subspecies diagnostic subset, linkage map construction and quantitative trait locus (QTL) analysis of a japonica × indica F 2 population, and background profiling during marker-assisted backcrossing. Furthermore, we identified subspecies-specific SNPs and discuss their distribution and association with agronomic traits and subspecies differentiation. Our results indicate that these subspecies-specific SNPs were present in wild rice prior to domestication. This genotyping system will serve as an efficient and quick tool for genetic analysis and molecular breeding in rice.

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Section: Discussionmentioning

confidence: 99%

Development and application of indica–japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding

et al. 2020

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“…Previously, we performed phenotypic and genotypic evaluation for low temperature germinability in a germplasm panel of 180 japonica rice accessions from temperate areas of East Asia (South Korea, Japan, China and North Korea). The germplasm showed significant variation in seed germination rate and vigor under low temperature conditions (Hyun et al 2015). Among the four groups, accessions from Japan and N. Korea showed higher germination rates than those from S. Korea and China.…”

Section: Introductionmentioning

confidence: 95%

“…Single nucleotide polymorphisms (SNPs) currently have become the most popular genetic markers because they are stable, efficient and cost-effective for automation (Rafalski 2002;Duran et al 2009;Edwards and Batley 2010) and widely used in many breeding and research programs for applications such as the assessment and selection of germplasm for target traits. Recently, we developed four SNP markers for LTG from previously reported LTG QTLs located on chromosome 2, 4 and 11 and using sequencing data from 60 germplasm accessions (Hyun et al 2015). The markers, qLTG2-6, qLTG4-3, qLTG4b-1 and qLTG11-1, were strongly associated with LTG and their R 2 values were 0.175, 0.091, 0.190 and 0.083, respectively (Hyun et al 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Recently, we developed four SNP markers for LTG from previously reported LTG QTLs located on chromosome 2, 4 and 11 and using sequencing data from 60 germplasm accessions (Hyun et al 2015). The markers, qLTG2-6, qLTG4-3, qLTG4b-1 and qLTG11-1, were strongly associated with LTG and their R 2 values were 0.175, 0.091, 0.190 and 0.083, respectively (Hyun et al 2015). The comparison of the genotypes for the each of 25 tolerant and sensitive accessions for these four marker loci revealed that in tolerant (strong LTG) accessions the alternative allele is prevalent among the qLTG2-6 and qLTG4-3 loci while the reference allele occurs more frequently at qLTG4b-1 and qLTG11-1 loci.…”

Section: Introductionmentioning

confidence: 99%

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Selection of Tolerant Rice Germplasm Through Phenotypic and Genotypic Evaluation for Germination Under Low Temperatures

Hyun

Choi

Lee

et al. 2015

Plant Breed. Biotech.

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Low temperature germinability (LTG) is an important trait for stand establishment in the direct-seeding method of rice cultivation. In temperate growing regions, water temperature during sowing season is frequently below 15°C resulting in poor crop establishment. The objective of this study was to select enhanced rice germplasm for low temperature germinability. Association of the phenotype for LTG with the genotype for qLTG3-1, a major QTL for LTG, in japonica rice accessions (n = 180) from East Asia was conducted. A highly significant association was observed between qLTG3-1 alleles and tolerant (χ 2 = 56.617, P = 5.08E-13) or sensitive (χ 2 = 32.844, P = 7.38E-08) accessions. Association of genotype and phenotype suggested the germplasm panel used in this study were closely associated with cold environment at the germination stage. Genotypic data from 32 SNP markers derived from previously reported LTG QTLs showed a mean polymorphism information content (PIC) of 0.248 and an average gene diversity of 0.307. A neighbor-joining tree clustered 23 tolerant accessions into one group and the genotypic data for four of the markers revealed that all of these accessions had the alternative allele for the qLTG3-1 and qLTG2-6 markers and the reference allele at the qLTG11-1 marker. Sensitive accessions clustered into one group and harbored the reference allele at the qLTG4-3 marker. Finally, ten accessions were selected after phenotypic and genotypic evaluation for LTG and these temperate japonica cultivars or breeding lines may contribute to the breeding of rice varieties for direct-seeding systems.

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“…The main types of starch available in rice grains include amylose and amylopectin whose structure and relative content have important effects on many quality traits of rice. For instance,the relative abundance of amylose and amylopectin has a correlated effect on the appearance quality, processing quality, cooking quality, nutritional quality and eating quality of rice grains [10]. Storage protein content and amino acid content and their relative equilibrium are the most important factors determining the grain nutritional quality in rice [3]; [11], and the storage protein content will also affect its eating quality, processing quality and appearance quality in rice grain [12].…”

Section: Introductionmentioning

confidence: 99%

Untitled

2018

JBR

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Amino acids, vitamins and lipids are the important micronutrients in rice grains. Their synthesis and regulation have important effects on the normal growth and development in rice seeds. This review has mainly summarized the new advances in the synthesis and regulation of amino acids, vitamins and lipids in rice grains. Simultaneously, the challenges of the synthesis and accumulation of the micronutrients in rice grains were also discussed. This review provides important information for genetic improvement of grain quality in rice and, potentially, other staple cereals.

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Development of low-temperature germinability markers for evaluation of rice (Oryza sativa L.) germplasm

Cited by 12 publications

References 39 publications

Development and application of indica–japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding

Development and application of indica–japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding

Selection of Tolerant Rice Germplasm Through Phenotypic and Genotypic Evaluation for Germination Under Low Temperatures

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