Genome Wide Association Study on Development and Evolution of Glutinous Rice

Abstract Background: Glutinous rice as a special endosperm type is consumed as a staple food in East Asian countries by consumers’ preference. Genetic studies on glutinous rice could be conducive to improve rice quality and understand its development and evolution. Therefor，we sought to explore more genes related to glutinous by genome wide association study and research the formation history for glutinous .Results: Here, genome-wide association study was performed to explore the associated loci/genes underlying glutinous rice by using 2108 rice accessions. Combining the expression patterns analysis, 127, 81, and 48 candidate genes were identified to be associated with endosperm type in whole rice panel, indica, and japonica sub-populations. There were 32 genes, including three starch synthesis-related genes Wx, SSG6, and OsSSIIa, detected simultaneously in the whole rice panel and subpopulations, playing important role in determining glutinous rice. The combined haplotype analyses revealed that the waxy haplotypes combination of three genes mainly distributed in Southeast Asia (SEA), SEA islands (SER) and East Asia islands (EAR). Through population structure and genetic differentiation, we suggest that waxy haplotypes of the three genes firstly evolved or were directly inherited from wild rice in japonica, and then infiltrated into indica in SER, SEA and EAR. Conclusions: The cloning and natural variation analysis of waxy-related genes are of great significance for the genetic improvement of quality breeding and comprehend the history in glutinous rice. This work provides valuable information for further gene discovery and understanding the evolution and formation for glutinous rice in SEA, SER and EAR.

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Genome Wide Association Study on Development and Evolution of Glutinous Rice

10.21203/rs.3.rs-60218/v1 ◽

2020 ◽

Author(s):

Conghui Jiang ◽

Muhammad Abdul Rehman Rashid ◽

Yan Zhao

Keyword(s):

Association Study ◽

Wild Rice ◽

Genome Wide Association Study ◽

Expression Patterns ◽

Starch Synthesis ◽

Genome Wide Association ◽

Staple Food ◽

Glutinous Rice ◽

Genome Wide ◽

Development And Evolution

Abstract Background: As a globally known staple food, rice is well domesticated in the world. Various regions have different food preferences, which lead to design the goals for breeding programs. Glutinous rice as a special endosperm type is also consumed as a staple food in East Asian countries by consumers’ preference. Genetic studies on glutinous rice could be conducive to improve rice quality and understand its development and evolution. Genome-wide association study was performed to explore the associated loci/genes underlying glutinous rice by using 2108 rice accessions. Results: A total of 399, 262 and 156 annotated genes with significant loci were identified to be associated with endosperm type. By combining the expression patterns analysis, 127, 81, and 48 candidate genes were screened in whole rice panel, indica, and japonica sub-populations with moderate expression in seeds. There were 32 genes, including three starch synthesis-related genes Wx, SSG6, and OsSSIIa, detected simultaneously in the whole rice panel and subpopulations, playing important role in determining glutinous rice. The main waxy haplotypes of three starch synthesis-related genes were identified by haplotype analysis, while the combined haplotype analyses, revealed that the waxy combined haplotype mainly distributed in Southeast Asia (SEA), SEA islands (SER) and East Asia islands (EAR). Through population structure and genetic differentiation, we proposed the evolutionary model of waxy haplotypes of the three genes from wild rice to japonica, and then to indica.Conclusion: It was concluded that the waxy haplotypes of the three genes firstly generated (or were directly inherited from wild rice) in japonica, and then flowed into indica in SER, SEA and EAR. These results provide valuable information for further gene discovery and understanding the development and evolution for glutinous rice.

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Genome-wide association study (GWAS) of circulating liver enzymes identifies >300 novel variants with distinct tissue expression patterns and gene set enrichment

Journal of Hepatology ◽

10.1016/s0168-8278(20)32022-5 ◽

2020 ◽

Vol 73 ◽

pp. S787

Author(s):

Vincent Chen ◽

Xiaomeng Du ◽

Yanhua Chen ◽

Samuel Handelman ◽

Elizabeth Speliotes

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Liver Enzymes ◽

Expression Patterns ◽

Tissue Expression ◽

Genome Wide Association ◽

Gene Set Enrichment ◽

Gene Set ◽

Genome Wide ◽

Novel Variants

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Temporal dynamics of QTL effects on vegetative growth in Arabidopsis thaliana

10.1101/2020.06.11.145953 ◽

2020 ◽

Author(s):

Rhonda C. Meyer ◽

Kathleen Weigelt-Fischer ◽

Dominic Knoch ◽

Marc Heuermann ◽

Yusheng Zhao ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Association Study ◽

Vegetative Growth ◽

Molecular Mechanisms ◽

Genome Wide Association Study ◽

Temporal Dynamics ◽

Expression Patterns ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

ABSTRACTWe assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from seven to 18 days after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from image analysis and used to calculate relative growth rates (RGR). In addition, initial seed size was determined. The generated data sets were used jointly for a genome-wide association study that identified 238 marker-trait associations (MTAs) individually explaining up to 8 % of the total phenotypic variation. Co-localisation of MTAs occurred at 33 genomic positions. At 21 of these positions, sequential co-localisation of MTAs for two to nine consecutive days was observed. The detected MTAs for PLA and RGR could be grouped according to their temporal expression patterns, emphasising that temporal variation of MTA action can be observed even during the vegetative growth phase, a period of continuous formation and enlargement of seemingly similar rosette leaves. This indicates that causal genes may be differentially expressed in successive periods. Analyses of the temporal dynamics of biological processes are needed to gain important insight into the molecular mechanisms of growth-controlling processes in plants.HighlightA genome-wide association study including the factor time highlighted that early plant growth in Arabidopsis is governed by several medium and many small effect loci, most of which act only during short phases of two to nine days.

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Genome-wide association study of micronaire using a natural population of representative upland cotton (Gossypium hirsutum L.)

Journal of Cotton Research ◽

10.1186/s42397-021-00089-1 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Jikun SONG ◽

Wenfeng PEI ◽

Jianjiang MA ◽

Shuxian YANG ◽

Bing JIA ◽

...

Keyword(s):

Association Study ◽

Cotton Fiber ◽

Upland Cotton ◽

Genetic Improvement ◽

Genome Wide Association Study ◽

Expression Patterns ◽

Snp Array ◽

Genome Wide Association ◽

Internal Quality ◽

Genome Wide

Abstract Background Micronaire is a comprehensive index reflecting the fineness and maturity of cotton fiber. Micronaire is one of the important internal quality indicators of the cotton fiber and is closely related to the value of the cotton fiber. Understanding the genetic basis of micronaire is required for the genetic improvement of the trait. However, the genetic architecture of micronaire at the genomic level is unclear. The present genome-wide association study (GWAS) aimed to identify the genetic mechanism of the micronaire trait in 83 representative upland cotton lines grown in multiple environments. Results GWAS of micronaire used 83 upland cotton accessions assayed by a Cotton 63 K Illumina Infinium single nucleotide polymorphism (SNP) array. A total of 11 quantitative trait loci (QTLs) for micronaire were detected on 10 chromosomes. These 11 QTLs included 27 identified genes with specific expression patterns. A novel QTL, qFM-A12–1, included 12 significant SNPs, and GhFLA9 was identified as a candidate gene based on haplotype block analysis and on strong and direct linkage disequilibrium between the significantly related SNPs and gene. GhFLA9 was expressed at a high level during secondary wall thickening at 20∼25 days post-anthesis. The expression level of GhFLA9 was significantly higher in the low micronaire line (Msco-12) than that in the high micronaire line (Chuangyou-9). Conclusions This study provides a genetic reference for genetic improvement of cotton fiber micronaire and a foundation for verification of the functions of GhFLA9.

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