Interactive Effects of Vernalization and Photoperiod Loci on Phenological Traits and Grain Yield and Differentiation of Iranian Wheat Landraces and Cultivars

Alipour, Hadi; Abdi, Hossein

doi:10.1007/s00344-020-10260-8

Cited by 7 publications

(6 citation statements)

References 27 publications

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“…In the PPD-D1 -insensitive subgroup, however, significant SNP markers were detected in the close vicinities of VRN-A1 (5A), VRN-B1 (5B), and VRN-B3 (7B), which were not apparent either in the complete set of 188 wheat genotypes or in the PPD-D1 -sensitive subgroup ( Supplementary Table 6 ). This may indicate the epistatic interactions between the specific allele phases of VRN1 , VNR3 , and PPD1 ( Karsai et al., 2008 ; Kiss et al., 2014 ; Alipour and Abdi, 2021 ; Cao et al., 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…The application of GWAS in elite germplasms is generally limited to the identification of smaller-effect MTAs, as major-effect MTAs might have already become fixed within the modern wheat cultivars ( Salvi and Tuberosa, 2015 ). Thus, in modern wheat GWA populations originating from the same megaenvironment, some alleles of the major plant developmental genes may be fixed due to the breeding activities for better adaptation ( Eagles et al., 2010 ; Kiss et al., 2014 ; Alipour and Abdi, 2021 ; Benaouda et al., 2022 ). However, our results also demonstrate that the allele phases of the major plant developmental genes determine the sets of minor developmental loci effective on plant development and are thus detectable.…”

Section: Discussionmentioning

confidence: 99%

“…Worland et al (1998) stated that photoperiod insensitivity may benefit grain yield in years and locations with hotter and drier summers. Several experiments revealed the importance of the PPD-D1 insensitivity allele in abiotic stress tolerance, mostly via avoiding the stressful periods through accelerated plant development, which led to earlier heading and ripening with a decreased seed number per spike and, in some cases, higher thousand kernel weight (Liu et al, 2020;Alipour and Abdi, 2021;Dreisigacker et al, 2021). In this process, not only is the photoperiod an important environmental indicator but also the ambient temperature during the phase of intensive stem elongation (Gonzaĺez et al, 2005b;Borraś-Gelonch et al, 2012;Kiss et al, 2017).…”

Section: Effects Of Ppd-d1 and The Minor Plant Developmental Loci On ...mentioning

confidence: 99%

“…In the latter case, the difference in the level of various abiotic stresses may also confound the exact dissection of the associations. It has been established that allelic differences and their combinations in vernalization response ( VRN ) and photoperiod sensitivity ( PPD ) genes impact abiotic stress responses in temperate cereals ( Voss-Fels et al., 2018 ; Alipour and Abdi, 2021 ; Abu-Elenein et al., 2021 ; Gol et al., 2021 ; Ochagavía et al., 2022 ). However, very little is known about how the genes that synchronize the developmental phases affect the actual formation of grain yield within a growing environment.…”

Section: Introductionmentioning

confidence: 99%

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Effects of genetic components of plant development on yield-related traits in wheat (Triticum aestivum L.) under stress-free conditions

Horváth

Kiss²,

Berki³

et al. 2023

Front. Plant Sci.

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The dynamics of plant development not only has an impact on ecological adaptation but also contributes to the realization of genetically determined yield potentials in various environments. Dissecting the genetic determinants of plant development becomes urgent due to the global climate change, which can seriously affect and even disrupt the locally adapted developmental patterns. In order to determine the role plant developmental loci played in local adaptation and yield formation, a panel of 188 winter and facultative wheat cultivars from diverse geographic locations were characterized with the 15K Illumina Single Nucleotide Polymorphism (SNP) chip and functional markers of several plant developmental genes and included into a multiseason field experiment. Genome-wide association analyses were conducted on five consecutive developmental phases spanning from the first node appearance to full heading together with various grain yield–related parameters. The panel was balanced for the PPD-D1 photoperiod response gene, which facilitated the analyses in the two subsets of photoperiod-insensitive and -sensitive genotypes in addition to the complete panel. PPD-D1 was the single highest source, explaining 12.1%–19.0% of the phenotypic variation in the successive developmental phases. In addition, 21 minor developmental loci were identified, each one explaining only small portions of the variance, but, together, their effects amounted to 16.6%–50.6% of phenotypic variance. Eight loci (2A_27, 2A_727, 4A_570, 5B_315, 5B_520, 6A_26, 7A_1-(VRN-A3), and 7B_732) were independent of PPD-D1. Seven loci were only detectable in the PPD-D1-insensitive genetic background (1A_539, 1B_487, 2D_649, 4A_9, 5A_584-(VRN-A1), 5B_571-(VRN-B1), and 7B_3-(VRN-B3)), and six loci were only detectable in the sensitive background, specifically 2A_740, 2D_25, 3A_579, 3B_414, 7A_218, 7A_689, and 7B_538. The combination of PPD-D1 insensitivity and sensitivity with the extremities of early or late alleles in the corresponding minor developmental loci resulted in significantly altered and distinct plant developmental patterns with detectable outcomes on some yield-related traits. This study examines the possible significance of the above results in ecological adaptation.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Effects Of Ppd-d1 and The Minor Plant Developmental Loci On ...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Effects of genetic components of plant development on yield-related traits in wheat (Triticum aestivum L.) under stress-free conditions

Horváth

Kiss²,

Berki³

et al. 2023

Front. Plant Sci.

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“…PCA aims to reduce data complexity in several principal components (PC). This multivariate method, in addition to studies of phenotypic and molecular diversity 2 , 3 , has been used in confirming population structure 4 , 5 , genotype selection 6 , understanding the pattern of genotype-by-environment interactions 7 , 8 , and selection of traits for yield modeling 9 . Despite its widespread use, the results of this technique can be highly biased in population genetic research 10 and GWAS 11 , which have been cited as potential pitfalls 12 .…”

Section: Introductionmentioning

confidence: 99%

Identification of novel putative alleles related to important agronomic traits of wheat using robust strategies in GWAS

Abdi

Alipour

Bernousi

et al. 2023

Sci Rep

Self Cite

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Principal component analysis (PCA) is widely used in various genetics studies. In this study, the role of classical PCA (cPCA) and robust PCA (rPCA) was evaluated explicitly in genome-wide association studies (GWAS). We evaluated 294 wheat genotypes under well-watered and rain-fed, focusing on spike traits. First, we showed that some phenotypic and genotypic observations could be outliers based on cPCA and different rPCA algorithms (Proj, Grid, Hubert, and Locantore). Hubert’s method provided a better approach to identifying outliers, which helped to understand the nature of these samples. These outliers led to the deviation of the heritability of traits from the actual value. Then, we performed GWAS with 36,000 single nucleotide polymorphisms (SNPs) based on the traditional approach and two robust strategies. In the conventional approach and using the first three components of cPCA as population structure, 184 and 139 marker-trait associations (MTAs) were identified for five traits in well-watered and rain-fed environments, respectively. In the first robust strategy and when rPCA was used as population structure in GWAS, we observed that the Hubert and Grid methods identified new MTAs, especially for yield and spike weight on chromosomes 7A and 6B. In the second strategy, we followed the classical and robust principal component-based GWAS, where the first two PCs obtained from phenotypic variables were used instead of traits. In the recent strategy, despite the similarity between the methods, some new MTAs were identified that can be considered pleiotropic. Hubert's method provided a better linear combination of traits because it had the most MTAs in common with the traditional approach. Newly identified SNPs, including rs19833 (5B) and rs48316 (2B), were annotated with important genes with vital biological processes and molecular functions. The approaches presented in this study can reduce the misleading GWAS results caused by the adverse effect of outlier observations.

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Applying Genetic Biofortification for Screening of Iranian Bread Wheat Genotypes with High Grain Yield and Nutritional Quality

Rabieyan

Bihamta

Mostashari

et al. 2023

J Soil Sci Plant Nutr

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Interactive Effects of Vernalization and Photoperiod Loci on Phenological Traits and Grain Yield and Differentiation of Iranian Wheat Landraces and Cultivars

Cited by 7 publications

References 27 publications

Effects of genetic components of plant development on yield-related traits in wheat (Triticum aestivum L.) under stress-free conditions

Effects of genetic components of plant development on yield-related traits in wheat (Triticum aestivum L.) under stress-free conditions

Identification of novel putative alleles related to important agronomic traits of wheat using robust strategies in GWAS

Applying Genetic Biofortification for Screening of Iranian Bread Wheat Genotypes with High Grain Yield and Nutritional Quality

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