scholarly journals Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 30 ◽  
Author(s):  
Gwen Iris Descalsota-Empleo ◽  
Abd Aziz Shamsudin Noraziyah ◽  
Ian Paul Navea ◽  
Chongtae Chung ◽  
Maria Stefanie Dwiyanti ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Analysis ◽  
Leaf Blight ◽  
Genome Wide Association ◽  
Anthocyanin Content ◽  
Phenotypic Variance ◽  
Genome Wide Association Analysis ◽  
Genome Wide ◽  
Colored Rice ◽  
Resistance Traits

Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.

scholarly journals Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm

Rice ◽  
2017 ◽  
Vol 10 (1) ◽  
Author(s):  
Christine Jade Dilla-Ermita ◽  
Erwin Tandayu ◽  
Venice Margarette Juanillas ◽  
Jeffrey Detras ◽  
Dennis Nicuh Lozada ◽  
...  
Keyword(s):  
Association Analysis ◽  
Leaf Blight ◽  
Genome Wide Association ◽  
Bacterial Leaf Blight ◽  
Blight Resistance ◽  
Genome Wide Association Analysis ◽  
Genome Wide

scholarly journals Genome-wide Association Analysis of Red Flesh Character Based on Resequencing Approach in Peach

2019 ◽  
Vol 144 (3) ◽  
pp. 209-216
Author(s):  
Huihui Liu ◽  
Ke Cao ◽  
Gengrui Zhu ◽  
Weichao Fang ◽  
Changwen Chen ◽  
...  
Keyword(s):  
Association Analysis ◽  
Anthocyanin Biosynthesis ◽  
Sugar Transport ◽  
Genome Wide Association ◽  
Chromosome 1 ◽  
Anthocyanin Content ◽  
Gene Encoding ◽  
Genome Wide Association Analysis ◽  
Genome Wide ◽  
A Genome

Anthocyanins are important molecules that are responsible for fruit color formation and are also beneficial to human health. To date, numerous structural and regulatory genes associated with anthocyanin biosynthesis in peach (Prunus persica) have been reported based on linkage analysis. In this study, we sought to identify further genes associated with anthocyanin content in peach by conducting a genome-wide association analysis of 129 peach accessions to detect markers associated with the trait. Significant association signals were detected when anthocyanin content was considered a qualitative character but not when it was considered a quantitative trait. We detected an association region located between 11.7 and 13.1 Mb in chromosome 1, a region in which only 133 of 146 genes have previously been functionally annotated. Gene ontology annotation of the genes in this region showed that membrane-associated genes (including one gene encoding a chloride channel protein and 17 sugar transport/carrier-associated genes) were significantly enriched, and we focused on these in subsequent analyses. Based on in vitro induction of anthocyanins in fruit flesh using different exogenously applied sugars and subsequent culture, we found that the expression level of 3 of the 18 membrane-associated genes, Prupe.1G156300, Prupe.1G156900, and Prupe.1G157000, increased during induction treatment. Furthermore, during the fruit development period of a white-fleshed and a red-fleshed peach cultivar, the expression of one gene encoding a transmembrane sugar transport protein was observed to be positively correlated with anthocyanin biosynthesis. These results will facilitate understanding of the molecular mechanism of anthocyanin biosynthesis in peach.

Molecular characterization of QTL-allele system for drought tolerance at seedling stage and optimal genotype design using multi-locus multi-allele genome-wide association analysis in a half-sib population of soybean [Glycine max (L.) Merr.]

2020 ◽  
pp. 1-12
Author(s):  
Mueen Alam Khan ◽  
Fei Tong ◽  
Wubin Wang ◽  
Jianbo He ◽  
Tuanjie Zhao ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Association Analysis ◽  
Genetic Architecture ◽  
Weighted Average ◽  
Genome Wide Association ◽  
Sand Culture ◽  
Phenotypic Variance ◽  
Potential Candidate ◽  
Genome Wide Association Analysis ◽  
Genome Wide

Abstract Characterizing the whole genetic architecture of drought tolerance (DT) is a persistent challenge for the breeders. Here we developed a half-sib population comprising of 404 lines of two recombinant inbred line (RIL) populations with M8206 as the joint parent (M8206 × TongShan and ZhengYang × M8206) and tested for its DT under sand culture. The population was sequenced using restriction-site-associated DNA sequencing filtered with minor allele frequency ≥0.01; 55,936 single nucleotide polymorphisms (SNPs) were obtained and assembled into 6137 SNPLDBs (SNP linkage disequilibrium blocks). The restricted two-stage multi-locus genome-wide association analysis characterized with error and false-positive control identified 40 QTLs with 93 alleles on an average of 34.75% of the phenotypic variance (PV) collectively for relative root length (RRL) and relative shoot length (RSL) that served as potential DT indicators. Among these, eight loci corresponded to previously reported QTLs, whereas 32 loci were therefore novel. The identified QTLs with their corresponding alleles for RRL and RSL were organized into QTL-allele matrices, depicting the comprehensive DT genetic architecture of the three parents/half-sib population. From the matrices, we predicted the possible best/optimal genotype with weighted average value (WAV) 1.553 over two indicators, while for the top 10 single crosses among RILs with 95th percentile WAV was 1.218–1.257, transgressive over the parents (0.693–0.794) yet much less than 1.553. From the detected QTL-allele system, 65 potential candidate genes collectively for both indicators explaining on an average of 24.41% PV were annotated and χ2-tested as a DT candidate gene system involving nine biological processes.

A Caution in Association of ABO Blood Group with COVID-19

2020 ◽  
Keyword(s):  
Gene Cluster ◽  
Clinical Outcomes ◽  
Blood Group ◽  
Association Analysis ◽  
Blood Type ◽  
Genome Wide Association ◽  
Chromosome 3 ◽  
Abo Blood Group ◽  
Genome Wide Association Analysis ◽  
Genome Wide

A comment on Zhao J, Yang Y, Huang H, Li D, Gu D, Lu X, et al. Association of ABO blood group and Covid19 susceptability. medRxiv [PREPRINT]. 2020; https://doi.org/10.1101/2020.03.11.20031096. Zeng X, Fan H, Lu D, Huang F, Meng X, Li Z, et al. Association between ABO blood group and clinical outcomes of Covid19. medRxiv[PREPRINT].2020; https://doi.org/10.1101/2020.04.15.20063107. Zietz M, Tatonetti N. Testing the association between blood type and COVID-19 infection, intubation, and death medRxiv [PREPRINT]. 2020; https://doi.org/10.1101/2020.04.08.20058073. Ellinghaus D, Degenhardt F, Bujanda L, al. e. The ABO blood group and a chromosome 3 gene cluster associate with SRAS-CoV2 respitarory failure in an Italy-Spain genome-wide association analysis. medRxiv. 2020; https://doi.org/10.1101/2020.05.31.20114991.

Genome-wide Association Analysis of Kernel Row Number in Maize

2014 ◽  
Vol 40 (1) ◽  
pp. 1 ◽  
Author(s):  
Huan-Xin ZHANG ◽  
Jian-Feng WENG ◽  
Xiao-Cong ZHANG ◽  
Chang-Lin LIU ◽  
Hong-Jun YONG ◽  
...  
Keyword(s):  
Association Analysis ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Genome Wide ◽  
Kernel Row Number
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