scholarly journals Genome-wide association study of low nitrogen tolerance traits at the seedling stage of rapeseed

2021 ◽  
Vol 65 ◽  
pp. 10-18
Author(s):  
C.L. ZENG ◽  
H.P. WAN ◽  
X.M. WU ◽  
X.G. DAI ◽  
J.D. CHEN ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Low Nitrogen Tolerance ◽  
Low Nitrogen

scholarly journals Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 318
Author(s):  
Tae-Ho Ham ◽  
Yebin Kwon ◽  
Yoonjung Lee ◽  
Jisu Choi ◽  
Joohyun Lee
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Matrix Analysis ◽  
Rice Seedlings ◽  
Genome Wide ◽  
A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

scholarly journals Genome-Wide Association Study of Rice Rooting Ability at the Seedling Stage

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Xin Xu ◽  
Junhua Ye ◽  
Yingying Yang ◽  
Mengchen Zhang ◽  
Qun Xu ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Rooting Ability ◽  
Genome Wide

scholarly journals Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 559
Author(s):  
Ashutosh Kumar Yadav ◽  
Aruna Kumar ◽  
Nitasha Grover ◽  
Ranjith Kumar Ellur ◽  
Haritha Bollinedi ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Salinity Tolerance ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
High Yield ◽  
Genome Wide ◽  
Trait Associations

Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker–trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.

scholarly journals Genome-Wide Association Study Identified Novel Genomic Loci Controlling Internode Lengths and Plant Height in Common Wheat under Different Nitrogen Treatments

2021 ◽  
Author(s):  
Piyi Xing ◽  
Xia Zhang ◽  
Dandan Li ◽  
Honggang Wang ◽  
Yinguang Bao ◽  
...  
Keyword(s):  
Association Study ◽  
Plant Height ◽  
Genome Wide Association Study ◽  
Nitrogen Deficiency ◽  
Internode Length ◽  
Spike Length ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Low Nitrogen

Abstract Nitrogen is an important nutrient for crop growth and development. Plant height-related traits can be affected by nitrogen supplementation. In this study, we performed a genome-wide association study (GWAS) on plant height, spike length, length of different internodes, and lodging resistance strength at the grain-filling stage based on a natural wheat population subjected to low nitrogen and normal (CK) treatments. GWAS analysis showed that a total of 86 quantitative trait locus (QTLs) were detected, including 13 QTLs for plant height, 10 QTLs for spike length, 19 QTLs for the length of the first internode from the top of the plant, 6 QTLs for the second internode length, 11 QTLs for the third internode length, 13 QTLs for the fourth internode length, and 14 QTLs for the fifth internode length. Compared to the CK treatment, the plant height, spike length, and fourth and fifth internode lengths were significantly affected by the low nitrogen treatment. A total of 18 QTLs responding to low nitrogen stress were detected, including three QTLs for the fourth internode length detected on 3A, 6A, and 6D chromosomes, eleven QTLs for the fifth internode length on 1A, 1B, 1D, 2A, 2B, 3A, 3B, 4A, 5B and 7B chromosomes, one QTL for spike length on 3A chromosome, and one QTL for plant height on 5B chromosome. These QTLs will enhance our understanding of the genetic basis of plant height responses to nitrogen deficiency and will benefit genetic reactions to nitrogen fertilization.

scholarly journals Genome-Wide Association Study of Root Development at the Seedling Stage in Korean Landrace Rice

2021 ◽  
Vol 53 (4) ◽  
pp. 424-431
Author(s):  
Jeonghwan Seo ◽  
Hongjia Zhang ◽  
Ah-Rim Lee ◽  
Wondo Lee ◽  
Yoo-Hyun Cho ◽  
...  
Keyword(s):  
Association Study ◽  
Root Development ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Genome Wide
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