scholarly journals Tomato SD1, encoding a kinase-interacting protein, is a major locus controlling stem development

2020 ◽  
Vol 71 (12) ◽  
pp. 3575-3587
Author(s):  
Jie Ye ◽  
Ranwen Tian ◽  
Xiangfei Meng ◽  
Peiwen Tao ◽  
Changxing Li ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Fruit Size ◽  
Stem Diameter ◽  
Chromosome 9 ◽  
High Yield ◽  
Evolutionary Analysis ◽  
Long Distance ◽  
Interacting Protein ◽  
A Genome ◽  
Stem Development

Abstract Stems serve as key determinants of plant development by connecting and supporting parts of the plant body, transporting nutrients important for long-distance communication that affect crop yield, and producing new organs. Nonetheless, studies on the regulation of stem development in crops are rather limited. Here, we found a significant correlation (P<0.001) between stem diameter (SD) and fruit size in tomato (Solanum lycopersicum). We performed a genome-wide association study and identified a novel quantitative trait locus (QTL), SDR9 (stem diameter regulator on CHROMOSOME 9), that co-localized with a gene encoding a kinase-interacting family protein (KIP), which is the most likely candidate gene related to SD (hereafter referred to as SD1). Overexpression of SD1 in thin-stem accessions resulted in increased SD. In contrast, suppressed expression of SD1 in thick-stem accessions using RNA interference exhibited the opposite effect. Further microscopic analyses showed that SD1 affected the stem diameter by controlling the size and number of secondary phloem cells. An 11-bp indel in the promoter region of SD1 that disrupts a gibberellin-responsive cis-element was linked to SD. Expression analysis revealed that SD1 was mainly expressed at the cambium of the stem and positively regulates stem development. Evolutionary analysis revealed that the thick-stem allele of SD1 was selected during the recent process of tomato improvement. Our results provide novel genetic and molecular insight into natural variation of SD in tomato and may accelerate the breeding of high yield tomato.

scholarly journals FLOURY ENDOSPERM19 encoding a class I glutamine amidotransferase affects grain quality in rice

2021 ◽  
Author(s):  
Guangming Lou ◽  
Pingli Chen ◽  
Hao Zhou ◽  
Pingbo Li ◽  
Jiawang Xiong ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Class I ◽  
High Yield ◽  
Eating Quality ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Rice Quality ◽  
Appearance Quality ◽  
A Genome ◽  
Glutamine Amidotransferase

Abstract As a staple food for more than half of the world’s population, the importance of rice is self-evident. Compared with ordinary rice, rice cultivars with superior eating quality and appearance quality are more popular with consumers due to its unique taste and ornamental value, even if their price is much higher. Appearance quality and CEQ (cooking and eating quality) are two very important aspects in the evaluation of rice quality. Here, we performed a genome-wide association study on chalkiness rate in a diverse panel of 533 cultivated rice accessions. We identified a batch of potential chalky genes and prioritize one (LOC_Os03g48060) for functional analyses. Two floury outer endosperm mutants (flo19-1 and flo19-2) were generated through editing LOC_Os03g48060 (named as FLO19 in this study), which encodes a class I glutamine amidotransferase. The different performance of the two mutants in various storage substances directly led to completely different changes in CEQ. The mutation of FLO19 gene caused the damage of carbon and nitrogen metabolism in rice, which affected the normal growth and development of rice, including decreased plant height and yield loss by decreased grain filling rate. Through haplotype analysis, we identified a haplotype of FLO19 that can improve both CEQ and appearance quality of rice, Hap2, which provides a selection target for rice quality improvement, especially for high-yield indica rice varieties.

scholarly journals A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.)

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 759 ◽  
Author(s):  
Caleb Manamik Breria ◽  
Ching-Hsiang Hsieh ◽  
Tsair-Bor Yen ◽  
Jo-Yi Yen ◽  
Thomas J. Noble ◽  
...  
Keyword(s):  
Salt Stress ◽  
Association Study ◽  
Stress Tolerance ◽  
Vigna Radiata ◽  
Genome Wide Association Study ◽  
Chromosome 9 ◽  
Genome Wide Association ◽  
Salt Stress Tolerance ◽  
Genome Wide ◽  
A Genome

Mungbean (Vigna radiata (L.) R. Wilzeck var. radiata) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a glycophyte than cereals. A significant portion of the global arable land is either salt or sodium affected. Thus, studies to understand and improve salt-stress tolerance are imminent. Here, we conducted a genome-wide association study (GWAS) to mine genomic loci underlying salt-stress tolerance during seed germination of mungbean. The World Vegetable Center (WorldVeg) mungbean minicore collection representing the diversity of mungbean germplasm was utilized as the study panel and variation for salt stress tolerance was found in this germplasm collection. The germplasm panel was classed into two agro-climatic groups and showed significant differences in their germination abilities under salt stress. A total of 5288 SNP markers obtained through genotyping-by-sequencing (GBS) were used to mine alleles associated with salt stress tolerance. Associated SNPs were identified on chromosomes 7 and 9. The associated region at chromosome 7 (position 2,696,072 to 2,809,200 bp) contains the gene Vradi07g01630, which was annotated as the ammonium transport protein (AMT). The associated region in chromosome 9 (position 19,390,227 bp to 20,321,817 bp) contained the genes Vradi09g09510 and Vradi09g09600, annotated as OsGrx_S16-glutaredoxin subgroup II and dnaJ domain proteins respectively. These proteins were reported to have functions related to salt-stress tolerance.

scholarly journals Integration of genome-wide association study and expression quantitative trait locus mapping for identification of endometriosis-associated genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ya-Ching Chou ◽  
Ming-Jer Chen ◽  
Pi-Hua Chen ◽  
Ching-Wen Chang ◽  
Mu-Hsien Yu ◽  
...  
Keyword(s):  
Association Study ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Chromosome 9 ◽  
Genome Wide Association ◽  
Chromosome 1 ◽  
Eqtl Analysis ◽  
Taiwanese Population ◽  
Genome Wide ◽  
A Genome

AbstractTo determine whether genetic predisposition to endometriosis varies depending on ethnicity and in association with expression quantitative trait loci (eQTL) in a Taiwanese population. We conducted a genome-wide association study (GWAS) and replicated it in 259 individuals with laparoscopy-confirmed stage III or IV endometriosis (cases) and 171 women without endometriosis (controls). Their genomic DNA was extracted from blood and evaluated by the GWAS of Taiwan Biobank Array. Novel genetic variants that predispose individuals to endometriosis were identified using GWAS and replication, including rs10739199 (P = 6.75 × 10−5) and rs2025392 (P = 8.01 × 10−5) at chromosome 9, rs1998998 (P = 6.5 × 10−6) at chromosome 14, and rs6576560 (P = 9.7 × 10−6) at chromosome 15. After imputation, strong signals were exhibited by rs10822312 (P = 1.80 × 10−7) at chromosome 10, rs58991632 (P = 1.92 × 10−6) and rs2273422 (P = 2.42 × 10−6) at chromosome 20, and rs12566078 (P = 2.5 × 10−6) at chromosome 1. We used the Genotype-Tissue Expression (GTEx) database to observe eQTL. Among these SNPs, the cis-eQTL rs13126673 of inturned planar cell polarity protein (INTU) showed significant association with INTU expression (P = 5.1 × 10–33). Moreover, the eQTL analysis was performed on endometriotic tissues from women with endometriosis. The expression of INTU in 78 endometriotic tissue of women with endometriosis is associated with rs13126673 genotype (P = 0.034). To our knowledge, this is the first GWAS to link endometriosis and eQTL in a Taiwanese population.

scholarly journals A Major Role for Common Genetic Variation in Anxiety Disorders

2017 ◽  
Author(s):  
Kirstin L. Purves ◽  
Jonathan R. I. Coleman ◽  
Sandra M. Meier ◽  
Christopher Rayner ◽  
Katrina A. S. Davis ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Anxiety Disorder ◽  
Anxiety Disorders ◽  
Genome Wide Association Study ◽  
Genetic Correlations ◽  
Anxiety Symptoms ◽  
Chromosome 9 ◽  
Common Genetic Variation ◽  
Genome Wide ◽  
A Genome

AbstractAnxiety disorders are common, complex psychiatric disorders with twin heritabilities of 30-60%. We conducted a genome-wide association study of Lifetime Anxiety Disorder (n = 83 565) and an additional Current Anxiety Symptoms (n= 77 125) analysis. The liability scale common variant heritability estimate for Lifetime Anxiety Disorder was 26%, and for Current Anxiety Symptoms was 31%. Five novel genome-wide significant loci were identified including an intergenic region on chromosome 9 that has previously been associated with neuroticism, and a locus overlapping the BDNF receptor gene, NTRK2. Anxiety showed significant genetic correlations with depression and insomnia as well as coronary artery disease, mirroring findings from epidemiological studies. We conclude that common genetic variation accounts for a substantive proportion of the genetic architecture underlying anxiety.

scholarly journals Combination of favorable gene haplotypes plays an important role in rice hybrid grain quality traits based on genome-wide association analysis

2020 ◽  
Author(s):  
Lanzhi Li ◽  
Xingfei Zheng ◽  
Xueli Zhang ◽  
Kai Xu ◽  
Shufeng Song ◽  
...  
Keyword(s):  
Grain Quality ◽  
Genome Wide Association Study ◽  
Amylose Content ◽  
Genome Wide Association ◽  
High Yield ◽  
Quality Trait ◽  
Rice Grain ◽  
Quality Traits ◽  
Genome Wide ◽  
A Genome

SummaryYield level and grain quality determine the commercial potential of rice (Oryza sativa L.) varieties. Mining and using genes that control important rice grain quality characteristics are major tasks for plant breeders. Here, a genome-wide association study was conducted to determine the genetic bases of 12 rice grain quality traits in 113 varieties and 565 testcross hybrids. A total of 56 significant SNPs were associated with 9 of the traits in variety phenotypic, general combining ability, testcross hybrid phenotypic and mid-parental heterotic datasets, from which 45 novel loci were identified. The cumulative effects of superior alleles or favorable haplotypes of genes closest to significant quality trait-associated loci were found in the four datasets. Additionally, the favorable gene haplotypes performed better than those of superior alleles in the variety and testcross hybrid datasets. Pyramiding the favorable haplotypes of five cloned rice grain quality genes resulted in a very low amylose content and high yield in the latter. These testcross hybrids had rice grain qualities similar to their parental lines but with much higher yields. The amylose content, grain width and grain length predictions for potential hybrids among the 113 varieties using genomic selection based on the BayesB method revealed a performance trend similar to those the testcross hybrids in our study. Thus, the selection of combination of favorable rice quality-related gene haplotypes is recommended to breed hybrids with high yields and elite grain qualities.

scholarly journals Effect of Longevity Genetic Variants on the Molecular Aging Rate

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 852-852
Author(s):  
Paola Sebastiani ◽  
Anastasia Gurinovich ◽  
Zeyuan Song ◽  
William Zhang ◽  
Stefano Monti ◽  
...  
Keyword(s):  
Association Study ◽  
Genetic Variants ◽  
Genome Wide Association Study ◽  
Serum Proteins ◽  
Chromosome 9 ◽  
Genome Wide Association ◽  
Biomarkers Of Aging ◽  
Genome Wide ◽  
A Genome ◽  
Protein Signature

Abstract We conducted a genome-wide association study of 1317 centenarians from the New England Centenarian Study and 2885 controls using >9M genetic variants. The most significantly associated variants were correlated to 4131 serum proteins in 224 study participants. The genetic and protein associations were replicated in a genome-wide association study of 480 centenarians and ~800 controls of Ashkenazy Jewish descent and a proteomic scan of approximately 1000 participants of the same study. The analysis replicated a protein signature associated with APOE genotypes and confirmed strong overexpression of BIRC2 (p < 5E-16) and underexpression of APOB in carriers of the APOE2 allele (p< 0.05). The analysis also discovered and replicated associations between longevity variants and slower changes of protein biomarkers of aging, including a novel protein signature of rs2184061 (CDKN2a/CDKN2B in chromosome 9). The analyses show that longevity variants correlate with proteome signatures that could be manipulated to discover healthy aging targets.

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