Genome-Wide Association Study Reveals the Genetic Basis of Five Quality Traits in Chinese Wheat

Shen, Hao; Lou, Hongyao; Wang, Haiwei; Shi, Jinghong; Liú, Dan; Baogerile,; Tao, Jianguang; Miao, Sanming; Pei, Qunce; Yu, Liangliang; Wu, Michael; Gao, Ming; Zhao, Naihu; Dong, Jin‐Chao; You, Minsheng; Xin, Mingming

doi:10.3389/fpls.2022.835306

Cited by 10 publications

(13 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Two QTL hotspots (3B.5 and 4B.5) were in similar positions to those reported by Yang et al (2019) in a Chinese winter wheat collection, but they did not share common traits. The study reported by (Hao et al, 2022) also with a collection of Chinese breeding lines that shared three regions, 2B.1, 3D.1, and 4B.5, although the last one reported an association with yield in our study. Finally, when comparing our results with (Rathan et al, 2022), using a diverse panel including breeding lines, landraces, and synthetic lines, four common regions were observed: 1A.2, 3B.3, 3B.5, and 5B.1.…”

Section: Marker Trait Associationssupporting

confidence: 67%

Uncovering the genetic basis for quality traits in the Mediterranean old wheat germplasm and phenotypic and genomic prediction assessment by cross-validation test

Yannam

Lopes²,

Guzmán³

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

The release of new wheat varieties is based on two main characteristics, grain yield and quality, to meet the consumer’s demand. Identifying the genetic architecture for yield and key quality traits has wide attention for genetic improvement to meet the global requirement. In this sense, the use of landraces represents an impressive source of natural allelic variation. In this study, a genome-wide association analysis (GWAS) with PCA and kinship matrix was performed to detect QTLs in bread wheat for fifteen quality and agronomic traits using 170 diverse landraces from 24 Mediterranean countries in two years of field trials. A total of 53 QTL hotspots containing 165 significant marker-trait associations (MTAs) were located across the genome for quality and agronomical traits except for chromosome 2D. The major specific QTL hotspots for quality traits were QTL_3B.3 (13 MTAs with a mean PVE of 8.2%) and QTL_4A.3 (15 MTAs, mean PVE of 11.0%), and for yield-related traits were QTL_2B.1 (8 MTAs, mean PVE of 7.4%) and QTL_4B.2 (5 MTAs, mean PVE of 10.0%). A search for candidate genes (CG) identified 807 gene models within the QTL hotspots. Ten of these CGs were expressed specifically in grain supporting the role of identified QTLs in Landraces, associated to bread wheat quality traits and grain formation. A cross-validation approach within the collection was performed to calculate the accuracies of genomic prediction for quality and agronomical traits, ranging from -0.03 to 0.64 for quality and 0.46 to 0.65 for agronomic traits. In addition, five prediction equations using the phenotypic data were developed to predict bread loaf volume in landraces. The prediction ability varied from 0.67 to 0.82 depending on the complexity of the traits considered to predict loaf volume.

show abstract

Section: Marker Trait Associationssupporting

confidence: 67%

Uncovering the genetic basis for quality traits in the Mediterranean old wheat germplasm and phenotypic and genomic prediction assessment by cross-validation test

Yannam

Lopes²,

Guzmán³

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…A genome-wide association study (GWAS) is an effective approach to identify genomic regions associated with specific variants of complex traits, which could dissect more alleles compared with linkage analysis. Recently, GWAS has been widely used to detect important candidate genes associated with yield, quality, salt stress, and drought stress ( Reig-Valiente et al., 2018 ; Luo et al., 2021 ; Hao et al., 2022 ; Wu et al., 2022 ). In barley, many functional loci associated with agronomic traits ( Xu et al., 2018 ), salt stress tolerance ( Mwando et al., 2020 ), drought stress tolerance ( Tarawneh et al., 2020 ), grain quality ( Jia et al., 2021 ) and disease resistance ( Pan et al., 2022 ) have been identified by GWAS.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association scan and transcriptome analysis reveal candidate genes for waterlogging tolerance in cultivated barley

et al. 2022

View full text Add to dashboard Cite

Waterlogging is the primary abiotic factor that destabilizes the yield and quality of barley (Hordeum vulgare L.). However, the genetic basis of waterlogging tolerance remains poorly understood. In this study, we conducted a genome-wide association study (GWAS) by involving 106,131 single-nucleotide polymorphisms (SNPs) with a waterlogging score (WLS) of 250 barley accessions in two years. Out of 72 SNPs that were found to be associated with WLS, 34 were detected in at least two environments. We further performed the transcriptome analysis in root samples from TX9425 (waterlogging tolerant) and Franklin (waterlogging sensitive), resulting in the identification of 5,693 and 8,462 differentially expressed genes (DEGs) in these genotypes, respectively. The identified DEGs included various transcription factor (TF) genes, primarily including AP2/ERF, bZIP and MYB. By combining GWAS and RNA-seq, we identified 27 candidate genes associated with waterlogging, of which three TFs (HvDnaJ, HvMADS and HvERF1) were detected in multiple treatments. Moreover, by overexpressing barley HvERF1 in Arabidopsis, the transgenic lines were detected with enhanced waterlogging tolerance. Altogether, our results provide new insights into the genetic mechanisms of waterlogging, which have implications in the molecular breeding of waterlogging-tolerant barley varieties.

show abstract

“…Mergoum et al (2013) had found a stable locus of grain hardness at 23 Mb on chromosome 1A, named 2013_Mergoum_3 , which was 4.39 Mb–8.94 Mb away from AX-111028882 identified on chromosome 1A in this study, considered the same site of grain hardness for close distance [ 37 ]. The stable genetic locus of grain hardness was excavated at 42.55–49.23 Mb on chromosome 1A, and the locus qHA1A.1 discovered by Hao et al [ 34 ] at 54.5 Mb were close to each other, so they were considered as the same locus. It was further indicated that 23.00–54.50 MB on chromosome 1A played an important role on controlling grain hardness, which could be the focus of further research.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Analysis of Grain Hardness in Common Wheat

Cao

et al. 2023

Genes

View full text Add to dashboard Cite

The grain hardness index (HI) is one of the important reference bases for wheat quality and commodity properties; therefore, it is essential and useful to identify loci associated with the HI in wheat breeding. The grain hardness index of the natural population including 150 common wheat genotypes was measured in this study. The phenotypic data diversity of HI based on four environments and the best linear unbiased prediction (BLUP) was analyzed. The results showed that the grain HI of the natural population ranged from 15.00 to 83.00, the variation range was from 5.10% to 24.44%, and the correlation coefficient was 0.872–0.980. BLUP value was used to grade and assign the grain HI to hard wheat, mixed wheat, and soft wheat, and the assigned phenotypes were used for genome-wide association analysis. Two types of grain hardness index phenotypic values were used for genome-wide association analysis (GWAS) using a 55K SNP array. A total of five significant association loci (p < 0.001) were excavated, among which four loci could be detected in three or more environments. They were distributed on chromosomes 1A and 7D, and the phenotypic contribution rate was 7.52% to 10.66%. A total of 48 sites related to grain hardness were detected by the assignment method, among which five were stable genetic sites, distributed on chromosomes 1A(2), 3B(1), 4B(1), and 7D(1), with phenotypic contribution rates ranging from 7.63% to 11.12%. Of the five loci detected by the assignment method, two stable loci were co-located in the phenotypic mapping results of the hardness index. One of the loci was consistent with previous reports and located on chromosome 1A, and one locus was unreported on chromosome 7D. Therefore, it may be a feasible attempt to use the assignment method to conduct genome-wide association analysis of the grain hardness index. In this study, a total of five genetic loci for grain hardness stability were excavated, and two of the loci were located in the two phenotypic values, two of which were not reported.

show abstract

Genome-Wide Association Study Reveals the Genetic Basis of Five Quality Traits in Chinese Wheat

Cited by 10 publications

References 66 publications

Uncovering the genetic basis for quality traits in the Mediterranean old wheat germplasm and phenotypic and genomic prediction assessment by cross-validation test

Uncovering the genetic basis for quality traits in the Mediterranean old wheat germplasm and phenotypic and genomic prediction assessment by cross-validation test

Genome-wide association scan and transcriptome analysis reveal candidate genes for waterlogging tolerance in cultivated barley

Genome-Wide Association Analysis of Grain Hardness in Common Wheat

Contact Info

Product

Resources

About