Genome-Wide Association Study for Adaptation to Agronomic Plant Density: A Component of High Yield Potential in Spring Wheat

AbstractRice yield per plant has a complex genetic architecture, which is mainly determined by its three component traits: the number of grains per panicle (GPP), kilo-grain weight (KGW), and tillers per plant (TP). Exploring ideotype breeding based on selection for genetically less complex component traits is an alternative route for further improving rice production. To understand the genetic basis of the relationship between rice yield and component traits, we investigated the four traits of two rice hybrid populations (575 + 1495 F1) in different environments and conducted meta-analyses of genome-wide association study (meta-GWAS). In total, 3589 significant loci for three components traits were detected, while only 3 loci for yield were detected. It indicated that rice yield is mainly controlled by minor-effect loci and hardly to be identified. Selecting quantitative trait locus/gene affected component traits to further enhance yield is recommended. Mendelian randomization design is adopted to investigate the genetic effects of loci on yield through component traits and estimate the genetic relationship between rice yield and its component traits by these loci. The loci for GPP or TP mainly had a positive genetic effect on yield, but the loci for KGW with different direction effects (positive effect or negative effect). Additionally, TP (Beta = 1.865) has a greater effect on yield than KGW (Beta = 1.016) and GPP (Beta = 0.086). Five significant loci for component traits that had an indirect effect on yield were identified. Pyramiding superior alleles of the five loci revealed improved yield. A combination of direct and indirect effects may better contribute to the yield potential of rice. Our findings provided a rationale for using component traits as indirect indices to enhanced rice yield, which will be helpful for further understanding the genetic basis of yield and provide valuable information for improving rice yield potential.

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

Plants ◽

10.3390/plants10030559 ◽

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.

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Identification of Earliness Per Se Flowering Time Locus in Spring Wheat through a Genome-Wide Association Study

Crop Science ◽

10.2135/cropsci2016.01.0066 ◽

2016 ◽

Vol 56 (6) ◽

pp. 2962-2672 ◽

Cited By ~ 16

Author(s):

Sivakumar Sukumaran ◽

Marta S. Lopes ◽

Susanne Dreisigacker ◽

Laura E. Dixon ◽

Meluleki Zikhali ◽

...

Keyword(s):

Association Study ◽

Flowering Time ◽

Spring Wheat ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Earliness Per Se ◽

Genome Wide ◽

A Genome ◽

Per Se

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Genome-Wide Association Study of Powdery Mildew Resistance in Russian Spring Wheat (T. aestivum L.) Varieties

Russian Journal of Genetics ◽

10.1134/s1022795419110085 ◽

2019 ◽

Vol 55 (11) ◽

pp. 1360-1374 ◽

Cited By ~ 1

Author(s):

I. N. Leonova

Keyword(s):

Powdery Mildew ◽

Association Study ◽

Spring Wheat ◽

Powdery Mildew Resistance ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Mildew Resistance ◽

Genome Wide

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Genome‐wide Association Study of Agronomic Traits in a Spring‐Planted North American Elite Hard Red Spring Wheat Panel

Crop Science ◽

10.2135/cropsci2017.07.0423 ◽

2018 ◽

Vol 58 (5) ◽

pp. 1838-1852 ◽

Cited By ~ 8

Author(s):

Jayfred Godoy ◽

Shiferaw Gizaw ◽

Shiaoman Chao ◽

Nancy Blake ◽

Arron Carter ◽

...

Keyword(s):

Association Study ◽

Spring Wheat ◽

North American ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Genome Wide Association ◽

Hard Red Spring Wheat ◽

Genome Wide

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Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan

PeerJ ◽

10.7717/peerj.11857 ◽

2021 ◽

Vol 9 ◽

pp. e11857

Author(s):

Akerke Amalova ◽

Saule Abugalieva ◽

Adylkhan Babkenov ◽

Sandukash Babkenova ◽

Yerlan Turuspekov

Keyword(s):

Association Study ◽

Spring Wheat ◽

Marker Assisted Selection ◽

Genome Wide Association Study ◽

Snp Markers ◽

Genome Wide Association ◽

Northern Kazakhstan ◽

Genome Wide ◽

Rainfed Conditions ◽

Selection Approach

Background Bread wheat is the most important cereal in Kazakhstan, where it is grown on over 12 million hectares. One of the major constraints affecting wheat grain yield is drought due to the limited water supply. Hence, the development of drought-resistant cultivars is critical for ensuring food security in this country. Therefore, identifying quantitative trait loci (QTLs) associated with drought tolerance as an essential step in modern breeding activities, which rely on a marker-assisted selection approach. Methods A collection of 179 spring wheat accessions was tested under irrigated and rainfed conditions in Northern Kazakhstan over three years (2018, 2019, and 2020), during which data was collected on nine traits: heading date (HD), seed maturity date (SMD), plant height (PH), peduncle length (PL), number of productive spikes (NPS), spike length (SL), number of kernels per spike (NKS), thousand kernel weight (TKW), and kernels yield per m2 (YM2). The collection was genotyped using a 20,000 (20K) Illumina iSelect SNP array, and 8,662 polymorphic SNP markers were selected for a genome-wide association study (GWAS) to identify QTLs for targeted agronomic traits. Results Out of the total of 237 discovered QTLs, 50 were identified as being stable QTLs for irrigated and rainfed conditions in the Akmola region, Northern Kazakhstan; the identified QTLs were associated with all the studied traits except PH. The results indicate that nine QTLs for HD and 11 QTLs for SMD are presumably novel genetic factors identified in the irrigated and rainfed conditions of Northern Kazakhstan. The identified SNP markers of the QTLs for targeted traits in rainfed conditions can be applied to develop new competitive spring wheat cultivars in arid zones using a marker-assisted selection approach.

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