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 53 publications

(93 citation statements)

References 126 publications

(173 reference statements)

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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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“…The importance of nitrate and ammonium for plant growth is well known, and it has been demonstrated that ammonium uptake capacity and response of cytosolic glutamine synthetase to ammonium supply are key factors in the adaptation of ammonium nutrition in Arabidopsis thaliana [76]. Furthermore, several genes involved in nitrogen uptake, assimilation, and remobilization have been found under selection in durum wheat [77], revealing that natural and selective pressures, as well as random mutation and genetic drift, shaped the expression of nitrogen genes. The nitrogen compounds play a pivotal role in photosynthesis as signals in regulating the responses of plants to environmental changes, such as resistance of plants to adverse conditions, including water stress.…”

Section: High Throughput Snp Genotyping Reveals Patterns Of Genetic Dmentioning

confidence: 99%

Marginal Grapevine Germplasm from Apulia (Southern Italy) Represents an Unexplored Source of Genetic Diversity

et al. 2020

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The investigation on the genetic diversity of grapevine germplasm is crucial for a more efficient use of grapevine genetic resources in light of changing environmental conditions. Here, we used simple sequence repeats (SSRs) coupled with single nucleotide polymorphism (SNP) markers to disclose grapevine genetic diversity of a collection of Apulian minor/neglected genotypes. Their relationships with national or international cultivars were also examined. Genetic diversity was investigated using 10 SSR markers and 1,178 SNPs generated by genotyping by sequencing (GBS). Based on the SSR data, the 128 genotypes were classified into six main genetic clusters. Twenty-four putative cases of synonymy and 2 of misnamings were detected. Ten “unknown” autochthonous genotypes did not show high similarity to Apulian, national, or international varieties. We took advantage of available GBS-derived SNP data points for only forty genotypes to better investigate the genetic distance among them, identify private SNP alleles, and divergent loci putatively under selection. Based on SNP alleles, two interesting gene pools of minor/neglected Apulian samples were identified. Genetic divergence was investigated by FST and allowed the detection of loci capable of differentiating the gene pools. Overall, this work emphasizes the need for recovering the untapped genetic variability that characterizes minor/neglected grapevine Apulian genotypes and the requirement to preserve and use more efficiently grapevine genetic resources in breeding programs.

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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

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

Cited by 53 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

Marginal Grapevine Germplasm from Apulia (Southern Italy) Represents an Unexplored Source of Genetic Diversity

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

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