Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm

Taranto, Francesca; D’Agostino, Nunzio; Rodríguez, Mónica; Pavan, Stefano; Minervini, Anna Paola; Pecchioni, Nicola; Papa, Roberto; Vita, Pasquale De

doi:10.3389/fgene.2020.00217

Cited by 45 publications

(50 citation statements)

References 126 publications

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“…Since breeders select directly for earliness, a single trait that is affected by both Vrn and Ppd genes, it is likely that alleles shortening cycle length at both loci were selected simultaneously in breeding programs. This has been shown to be the case in recent studies conducted with Australian bread wheat (Joukhadar et al, 2019) and Italian durum wheat (Taranto et al, 2020) which have demonstrated that artificial selection involved strong simultaneous selection on specific alleles for vernalization and photoperiod genes.…”

Section: Effects Of the Vrn-1 And Ppd-1 Alleles And Allele Combinatiomentioning

confidence: 80%

Allelic Variation at the Vernalization Response (Vrn-1) and Photoperiod Sensitivity (Ppd-1) Genes and Their Association With the Development of Durum Wheat Landraces and Modern Cultivars

et al. 2020

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Wheat adaptability to a wide range of environmental conditions is mostly determined by allelic diversity within genes controlling vernalization requirement (Vrn-1) and photoperiod sensitivity (Ppd-1). We characterized a panel of 151 durum wheat Mediterranean landraces and 20 representative locally adapted modern cultivars for their allelic composition at Vrn-1 and Ppd-1 gene using diagnostic molecular markers and studied their association with the time needed to reach six growth stages under field conditions over 6 years. Compared with the more diverse and representative landrace collection, the set of modern cultivars were characterized by a reduction of 50% in the number of allelic variants at the Vrn-A1 and Vrn-B1 genes, and the high frequency of mutant alleles conferring photoperiod insensitivity at Ppd-A1, which resulted on a shorter cycle length. Vrn-A1 played a greater role than Vrn-B1 in regulating crop development (Vrn-A1 > Vrn-B1). The results suggest that mutations in the Vrn-A1 gene may have been the most important in establishing the spring growth habit of Mediterranean landraces and modern durum cultivars. The allele Vrn-A1d, found in 10 landraces, delayed development. The relative effects of single Vrn-A1 alleles on delaying the development of the landraces were vrn-A1 = Vrn-A1d > Vrn-A1b > Vrn-A1c. Allele vrn-B1 was present in all except two landraces and in all modern cultivars. The null allele at Ppd-A1 (a deletion first observed in the French bread wheat cultivar 'Capelle-Desprez') was found for the first time in durum wheat in the present study that identified it in 30 landraces from 13 Mediterranean countries. Allele Ppd-A1a (GS105) was detected in both germplasm types, while the allele Ppd-A1a (GS100) was found only in modern North American and Spanish cultivars. The relative effect of single Ppd-A1

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Section: Effects Of the Vrn-1 And Ppd-1 Alleles And Allele Combinatiomentioning

confidence: 80%

Allelic Variation at the Vernalization Response (Vrn-1) and Photoperiod Sensitivity (Ppd-1) Genes and Their Association With the Development of Durum Wheat Landraces and Modern Cultivars

et al. 2020

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“…Genetic structure (i.e., the occurrence of sub-populations with different allele frequencies) reflects remote differences in ancestry; in crops, it often originates from physical barriers to random mating and anthropic selection for specific traits, such as seed/fruit size and phenological features (Pavan et al, 2017(Pavan et al, , 2019Siol et al, 2017). Instead, kinship reflects recent ancestry, often related to pedigree connections among modern cultivars (Taranto et al, 2020).…”

Section: Checking For Sample Duplication and Ancestral Relationshipsmentioning

confidence: 99%

Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies

et al. 2020

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High-throughput genotyping boosts genome-wide association studies (GWAS) in crop species, leading to the identification of single-nucleotide polymorphisms (SNPs) associated with economically important traits. Choosing a cost-effective genotyping method for crop GWAS requires careful examination of several aspects, namely, the purpose and the scale of the study, crop-specific genomic features, and technical and economic matters associated with each genotyping option. Once genotypic data have been obtained, quality control (QC) procedures must be applied to avoid bias and false signals in genotype-phenotype association tests. QC for human GWAS has been extensively reviewed; however, QC for crop GWAS may require different actions, depending on the GWAS population type. Here, we review most popular genotyping methods based on next-generation sequencing (NGS) and array hybridization, and report observations that should guide the investigator in the choice of the genotyping method for crop GWAS. We provide recommendations to perform QC in crop species, and deliver an overview of bioinformatics tools that can be used to accomplish all needed tasks. Overall, this work aims to provide guidelines to harmonize those procedures leading to SNP datasets ready for crop GWAS.

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“…Specifically, nine additional yield components were considered: kernel length (KL), kernel width (KW), thousand-kernel weight (TKW) associated with the kernel weight, kernels number per spike (KNS), kernels number per spikelet (KNSL), spikelets number per spike (SLNS) associated with the kernels number, grain yield (GY), kernels number per square meter (KNM) and spike number per square meter (SNM) related to the kernels number per unit area ( Figure 1 ). Results from a study revealed that major well-known genes and/or QTLs affecting plant height (PH) and earliness which are related to grain yield traits co-localized with outlier SNP loci in a large panel of Italian durum wheat accessions [ 24 ]. Therefore, QTLs for plant height (PH) were also included ( Table S1 ).…”

Section: Genetics Of Grain Yield In Wheatmentioning

confidence: 99%

“…Different breeding approaches including quantitative trait loci (QTL) and genome-wide association studies (GWAS) are being applied to increase the grain yield potential of durum wheat through molecular marker-assisted selection (MAS). In fact, multiple QTLs with large and small effects have been mapped on all wheat chromosomes and they have been recently published [ 20 , 21 , 22 , 23 , 24 ]. Therefore, due to the importance of this complex trait and to summarize the available information on the genetics of grain yield in durum wheat, the objective of this review is to analyze in a comprehensive manner the most recent findings associated with the genetics, genomics and the identification of QTL for grain yield-related traits in durum wheat.…”

Section: Introductionmentioning

confidence: 99%

Molecular Mapping and Genomics of Grain Yield in Durum Wheat: A Review

Arriagada

Marcotuli

Gadaleta

et al. 2020

IJMS

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Durum wheat is the most relevant cereal for the whole of Mediterranean agriculture, due to its intrinsic adaptation to dryland and semi-arid environments and to its strong historical cultivation tradition. It is not only relevant for the primary production sector, but also for the food industry chains associated with it. In Mediterranean environments, wheat is mostly grown under rainfed conditions and the crop is frequently exposed to environmental stresses, with high temperatures and water scarcity especially during the grain filling period. For these reasons, and due to recurrent disease epidemics, Mediterranean wheat productivity often remains under potential levels. Many studies, using both linkage analysis (LA) and a genome-wide association study (GWAS), have identified the genomic regions controlling the grain yield and the associated markers that can be used for marker-assisted selection (MAS) programs. Here, we have summarized all the current studies identifying quantitative trait loci (QTLs) and/or candidate genes involved in the main traits linked to grain yield: kernel weight, number of kernels per spike and number of spikes per unit area.

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Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm

Cited by 45 publications

References 126 publications

Allelic Variation at the Vernalization Response (Vrn-1) and Photoperiod Sensitivity (Ppd-1) Genes and Their Association With the Development of Durum Wheat Landraces and Modern Cultivars

Allelic Variation at the Vernalization Response (Vrn-1) and Photoperiod Sensitivity (Ppd-1) Genes and Their Association With the Development of Durum Wheat Landraces and Modern Cultivars

Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies

Molecular Mapping and Genomics of Grain Yield in Durum Wheat: A Review

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