Genetic variation and association mapping of silica concentration in rice hulls using a germplasm collection

Proctor, A.; Hawkridge, M.; Jackson, Aaron; Yeater, Kathleen M.; Counce, Paul A.; Wang, Yan; McClung, Anna M.; Fjellstrom, Robert G.

doi:10.1007/s10709-012-9637-x

Cited by 33 publications

(36 citation statements)

References 54 publications

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“…By comparison, the sample size used in this study is larger than used in the previous studies (Bryant et al 2011;Jia et al 2012;Courtois et al 2013). To primarily detect markers associated with seed germination and seedling growth under normal, drought and salt conditions, 159 SSR markers scattered on 12 chromosomes with an average interval of *10 cM were used in this study.…”

Section: Discussionmentioning

confidence: 99%

Association mapping of seed germination and seedling growth at three conditions in indica rice (Oryza sativa L.)

Jiaan

Yang

et al. 2015

Euphytica

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Seed germination and seedling establishment are critical phases in rice. In this study, 276 indica accessions were used to investigate the genetic control of seed germination and seedling growth under normal, drought and salt conditions by using the trait of germination percentage, germination index and seedling survival percentage. The significant natural variation of seed germination and seedling growth was observed among accessions at three conditions. Correlation analysis showed that the significant and positive relationship between drought and salt stress conditions was observed in seed germination while not in seedling growth. A total of 12, 14 and 9 simple sequence repeat (SSR) markers associated with three traits were identified under normal, drought and salt conditions respectively. Seven and two SSR loci were simultaneously identified at two and three conditions, respectively, five SSR loci each were specific for drought and salt stress condition. By comparing chromosomal positions of the markers here with previously studies, six SSR loci might represent novel. Several accessions with elite performance of seed germination and seedling growth under stress conditions were firstly identified, such as Gulfrose, Kaijiangliushizao, Yangxidao and Xincunheigu. Six cross combinations each for improving seed germination and seedling growth under stress conditions were predicted. The identified elite accessions and alleles might be applicable to improve rice seed germination and seedling growth by the marker-assisted selection approach.

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Section: Discussionmentioning

confidence: 99%

Association mapping of seed germination and seedling growth at three conditions in indica rice (Oryza sativa L.)

Jiaan

Yang

et al. 2015

Euphytica

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“…The GWAS mapping was conducted with 157 markers including 148 SSR markers, three InDel markers and six SNP markers (Bryant et al, 2011). Prior to conducting the GWAS based mapping analyses, the population structure was examined using the model-based program STRUCTURE (Pritchard et al, 2000) and Principal Component Analysis (PCA) using JMP Genomics in SAS was performed, summarizing the major patterns of variation in a multi-locus data set.…”

Section: Methodsmentioning

confidence: 99%

“…The extent of linkage disequilibrium (LD) was determined as the squared allele frequency correlation estimates ( r 2 , Weir, 1996) and to measure the significance of r 2 . The expected p -value versus the observed p -value test statistics for the SSR markers were plotted (Q-Q plot) to assess the control of type I (false positive) errors under multiple run parameters, as previously published for RMC accessions (Bryant et al, 2011; Li et al, 2011, 2012). A marker-trait association was determined to be significant when the p -value was p < 0.01.…”

Section: Methodsmentioning

confidence: 99%

“…Of the remaining 38 accessions, 24 were O. sativa accessions classified as an admixture of two or more subpopulation groups and 14 accessions represented other Oryza species, thus were not O. sativa (Li et al, 2010; personnel communication). This rich genetic diversity makes the RMC attractive for GWAS mapping, as demonstrated by the marker-trait associations already reported for grain yield and other harvest index components (Li et al, 2011), silica concentration (Bryant et al, 2011), harvest index (Li et al, 2012), resistance to rice sheath blight disease (Jia et al, 2012), protein content (Bryant et al, 2013), and pericarp color (Wang et al, 2016b). …”

Section: Introductionmentioning

confidence: 97%

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Assessment of Five Chilling Tolerance Traits and GWAS Mapping in Rice Using the USDA Mini-Core Collection

et al. 2017

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Rice (Oryza sativa L.) is often exposed to cool temperatures during spring planting in temperate climates. A better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. To dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. Based on these assays, five chilling tolerance indices were calculated and assessed using 202 O. sativa accessions from the Rice Mini-Core (RMC) collection. Significant differences between RMC accessions made the five indices suitable for genome-wide association study (GWAS) based quantitative trait loci (QTL) mapping. For young seedling stage indices, japonica and indica subspecies clustered into chilling tolerant and chilling sensitive accessions, respectively, while both subspecies had similar low temperature germinability distributions. Indica subspecies were shown to have chilling acclimation potential. GWAS mapping uncovered 48 QTL at 39 chromosome regions distributed across all 12 rice chromosomes. Interestingly, there was no overlap between the germination and seedling stage QTL. Also, 18 QTL and 32 QTL were in regions discovered in previously reported bi-parental and GWAS based QTL mapping studies, respectively. Two novel low temperature seedling survivability (LTSS)–QTL, qLTSS3-4 and qLTSS4-1, were not in a previously reported QTL region. QTL with strong effect alleles identified in this study will be useful for marker assisted breeding efforts to improve chilling tolerance in rice cultivars and enhance gene discovery for chilling tolerance.

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“…Association analysis is regarded as a powerful tool for trait-related marker screening23. Through this approach, multiple quantitative trait loci (QTLs) have been successfully identified in some species456. Genome-wide association study (GWAS) and candidate gene association study are two powerful strategies for association analyses.…”

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confidence: 99%

Gene set based association analyses for the WSSV resistance of Pacific white shrimp Litopenaeus vannamei

et al. 2017

Sci Rep

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White Spot Syndrome Virus (WSSV) is regarded as a virus with the strongest pathogenicity to shrimp. For the threshold trait such as disease resistance, marker assisted selection (MAS) was considered to be a more effective approach. In the present study, association analyses of single nucleotide polymorphisms (SNPs) located in a set of immune related genes were conducted to identify markers associated with WSSV resistance. SNPs were detected by bioinformatics analysis on RNA sequencing data generated by Illimina sequencing platform and Roche 454 sequencing technology. A total of 681 SNPs located in the exons of immune related genes were selected as candidate SNPs. Among these SNPs, 77 loci were genotyped in WSSV susceptible group and resistant group. Association analysis was performed based on logistic regression method under an additive and dominance model in GenABEL package. As a result, five SNPs showed associations with WSSV resistance at a significant level of 0.05. Besides, SNP-SNP interaction analysis was conducted. The combination of SNP loci in TRAF6, Cu/Zn SOD and nLvALF2 exhibited a significant effect on the WSSV resistance of shrimp. Gene expression analysis revealed that these SNPs might influence the expression of these immune-related genes. This study provides a useful method for performing MAS in shrimp.

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Genetic variation and association mapping of silica concentration in rice hulls using a germplasm collection

Cited by 33 publications

References 54 publications

Association mapping of seed germination and seedling growth at three conditions in indica rice (Oryza sativa L.)

Association mapping of seed germination and seedling growth at three conditions in indica rice (Oryza sativa L.)

Assessment of Five Chilling Tolerance Traits and GWAS Mapping in Rice Using the USDA Mini-Core Collection

Gene set based association analyses for the WSSV resistance of Pacific white shrimp Litopenaeus vannamei

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