Linkage and association mapping and Kompetitive allele-specific PCR marker development for improving grain protein content in wheat

Abstract Wheat grain protein content (GPC) is an important quality indicator. The GPC of wheat grown in the middle and lower reaches of the Yangtze River is often low. Marker-assisted selection (MAS) is an effective tool for improving quantitative traits; however, except Gpc-B1, most markers have not been effectively applied in GPC improvement, although many related loci have been identified. Linkage analysis using a recombinant inbred line population from the cross of core parents of Ningmai 9 and Yangmai 158 and association mapping using the local cultivated varieties were performed and nine candidate intervals were identified. The appropriate kompetitive allele specific PCR (KASP) markers associated with GPC were successfully developed and applied in 1163 F4 breeding lines. Three markers, Kgpc-2B, Kgpc-2D, and Kgpc-4A, were validated to be significantly related to GPC by large-scale association mapping, and they were combined to achieve the highest efficiency to enhance GPC. We applied these markers in 164 F6 breeding lines and obtained 15 lines with high GPC, indicating their high selective efficiency. Further, strategies for gene exploration in the three significant intervals were proposed. These results were expected to provide a novel route for improving GPC in wheat quality breeding.

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Genotyping-by-sequencing based single nucleotide polymorphisms enabled Kompetitive Allele Specific PCR marker development in mutant Rubus genotypes

Electronic Journal of Biotechnology ◽

10.1016/j.ejbt.2018.08.001 ◽

2018 ◽

Vol 35 ◽

pp. 57-62 ◽

Cited By ~ 5

Author(s):

Jaihyunk Ryu ◽

Woon Ji Kim ◽

Juhyun Im ◽

Sang Hun Kim ◽

Kang-Seop Lee ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Genotyping By Sequencing ◽

Marker Development ◽

Nucleotide Polymorphisms ◽

Pcr Marker ◽

Single Nucleotide ◽

Specific Pcr ◽

Allele Specific ◽

Allele Specific Pcr

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Kompetitive Allele-Specific PCR Marker Development and Quantitative Trait Locus Mapping for Bakanae Disease Resistance in Korean Japonica Rice Varieties

Plant Breeding and Biotechnology ◽

10.9787/pbb.2019.7.3.208 ◽

2019 ◽

Vol 7 (3) ◽

pp. 208-219 ◽

Cited By ~ 4

Author(s):

Kyeong-Seong Cheon ◽

Young-Min Jeong ◽

Youn-Young Lee ◽

Jun Oh ◽

Do-Yu Kang ◽

...

Keyword(s):

Japonica Rice ◽

Marker Development ◽

Pcr Marker ◽

Rice Varieties ◽

Bakanae Disease ◽

Specific Pcr ◽

Allele Specific ◽

Trait Locus ◽

Locus Mapping ◽

Allele Specific Pcr

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Isolation of a gibberellin-insensitive dwarfing gene, Rht-B1e, and development of an allele-specific PCR marker

Molecular Breeding ◽

10.1007/s11032-012-9730-y ◽

2012 ◽

Vol 30 (3) ◽

pp. 1443-1451 ◽

Cited By ~ 13

Author(s):

Aixia Li ◽

Wenlong Yang ◽

Xiaoli Guo ◽

Dongcheng Liu ◽

Jiazhu Sun ◽

...

Keyword(s):

Pcr Marker ◽

Dwarfing Gene ◽

Specific Pcr ◽

Allele Specific ◽

Allele Specific Pcr

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Genome-Wide Association Studies and Genomic Selection for Grain Protein Content Stability in a Nested Association Mapping Population of Spring Wheat

10.1101/2021.04.15.440064 ◽

2021 ◽

Author(s):

Karansher S. Sandhu ◽

Paul D. Mihalyov ◽

Megan J. Lewien ◽

Michael O. Pumphrey ◽

Arron H Carter

Keyword(s):

Association Mapping ◽

Protein Content ◽

Genomic Selection ◽

Genetic Control ◽

Spring Wheat ◽

Grain Protein Content ◽

Genome Wide Association ◽

Grain Protein ◽

Nested Association Mapping ◽

Genome Wide

Grain protein content (GPC) is controlled by complex genetic systems and their interactions, and is an important quality determinant for hard spring wheat as it has a positive effect on bread and pasta quality. GPC is variable among genotypes and strongly influenced by environment. Thus, understanding the genetic control of wheat GPC and identifying genotypes with improved stability is an important breeding goal. The objectives of this research were to identify genetic backgrounds with less variation for GPC across environments and identify quantitative trait loci (QTLs) controlling the stability of GPC. A spring wheat nested association mapping (NAM) population of 650 recombinant inbred lines (RIL) derived from 26 diverse founder parents crossed to one common parent, 'Berkut', was phenotyped over three years of field trials (2014-2016). Genomic selection models were developed and compared based on prediction of GPC and GPC stability. After observing variable genetic control of GPC within the NAM population, seven RIL families displaying reduced marker-by-environment interaction were selected based on a stability index derived from Finlay-Wilkinson regression. A genome-wide association study identified seven significant QTLs for GPC stability with a Bonferroni-adjusted P value <0.05. This study also demonstrated that genome-wide prediction of GPC with ridge regression best linear unbiased estimates reached up to r = 0.69. Genomic selection can be used to apply selection pressure for GPC and improve genetic gain for GPC.

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Genomic Selection and Genome-Wide Association Studies for Grain Protein Content Stability in a Nested Association Mapping Population of Wheat

Agronomy ◽

10.3390/agronomy11122528 ◽

2021 ◽

Vol 11 (12) ◽

pp. 2528

Author(s):

Karansher S. Sandhu ◽

Paul D. Mihalyov ◽

Megan J. Lewien ◽

Michael O. Pumphrey ◽

Arron H. Carter

Keyword(s):

Association Mapping ◽

Protein Content ◽

Genomic Selection ◽

Genetic Control ◽

Spring Wheat ◽

Grain Protein Content ◽

Genome Wide Association ◽

Grain Protein ◽

Nested Association Mapping ◽

Genome Wide

Grain protein content (GPC) is controlled by complex genetic systems and their interactions and is an important quality determinant for hard spring wheat as it has a positive effect on bread and pasta quality. GPC is variable among genotypes and strongly influenced by the environment. Thus, understanding the genetic control of wheat GPC and identifying genotypes with improved stability is an important breeding goal. The objectives of this research were to identify genetic backgrounds with less variation for GPC across environments and identify quantitative trait loci (QTLs) controlling the stability of GPC. A spring wheat nested association mapping (NAM) population of 650 recombinant inbred lines (RIL) derived from 26 diverse founder parents crossed to one common parent, ‘Berkut’, was phenotyped over three years of field trials (2014–2016). Genomic selection models were developed and compared based on predictions of GPC and GPC stability. After observing variable genetic control of GPC within the NAM population, seven RIL families displaying reduced marker-by-environment interaction were selected based on a stability index derived from a Finlay–Wilkinson regression. A genome-wide association study identified eighteen significant QTLs for GPC stability with a Bonferroni-adjusted p-value < 0.05 using four different models and out of these eighteen QTLs eight were identified by two or more GWAS models simultaneously. This study also demonstrated that genome-wide prediction of GPC with ridge regression best linear unbiased estimates reached up to r = 0.69. Genomic selection can be used to apply selection pressure for GPC and improve genetic gain for GPC.

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