Genetic diversity in historical and modern wheat varieties of the U.S. Pacific Northwest

Sthapit, Sajal; Marlowe, Karol; Covarrubias, Dolores C.; Ruff, Travis; Eagle, Jonathan D.; McGinty, Emma M.; Hooker, Marcus A.; Duong, Ngoc; Skinner, Daniel Z.; See, Deven R.

doi:10.1002/csc2.20299

Cited by 14 publications

(17 citation statements)

References 49 publications

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“…We first divided the breeding periods into six corresponding to the pre-1970s, 1971–1980, 1981–1990, 1991–2000, 2001–2010, and 2011–2018. We also tried to assess the extent of genetic variation and divergence across four breeding periods by taking into account some of the rationale used in previous similar studies in Canada 4 and the US 10 . The first period represents the cultivation of primarily introduced and old cultivars before the 1980s, followed by the second period that consisted of cultivars developed by breeders in Canada using conventional breeding methods between 1981 and 2000.…”

Section: Methodsmentioning

confidence: 99%

“…The impact of plant breeding on the genetic diversity of crops has been studied using diverse types of molecular markers, including simple sequence repeats (SSRs) or microsatellites 1 – 4 , expressed sequence tags 5 , 6 , and single nucleotide polymorphisms (SNP) generated through different genotyping platforms 7 – 10 . Results of the various molecular diversity studies shed some light on the impact of plant breeding on crops’ genetic diversity, but the results are inconsistent with the general perception that modern plant breeding reduces crop genetic diversity.…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array

Semagn

Iqbal

Alachiotis

et al. 2021

Sci Rep

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Previous molecular characterization studies conducted in Canadian wheat cultivars shed some light on the impact of plant breeding on genetic diversity, but the number of varieties and markers used was small. Here, we used 28,798 markers of the wheat 90K single nucleotide polymorphisms to (a) assess the extent of genetic diversity, relationship, population structure, and divergence among 174 historical and modern Canadian spring wheat varieties registered from 1905 to 2018 and 22 unregistered lines (hereinafter referred to as cultivars), and (b) identify genomic regions that had undergone selection. About 91% of the pairs of cultivars differed by 20–40% of the scored alleles, but only 7% of the pairs had kinship coefficients of < 0.250, suggesting the presence of a high proportion of redundancy in allelic composition. Although the 196 cultivars represented eight wheat classes, our results from phylogenetic, principal component, and the model-based population structure analyses revealed three groups, with no clear structure among most wheat classes, breeding programs, and breeding periods. FST statistics computed among different categorical variables showed little genetic differentiation (< 0.05) among breeding periods and breeding programs, but a diverse level of genetic differentiation among wheat classes and predicted groups. Diversity indices were the highest and lowest among cultivars registered from 1970 to 1980 and from 2011 to 2018, respectively. Using two outlier detection methods, we identified from 524 to 2314 SNPs and 41 selective sweeps of which some are close to genes with known phenotype, including plant height, photoperiodism, vernalization, gluten strength, and disease resistance.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array

Semagn

Iqbal

Alachiotis

et al. 2021

Sci Rep

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show abstract

“…More loci for SNS should thus be identified and utilized owing to its important role in yield formation. Nonetheless, common wheat breeding reduces the genetic diversity among elite germplasm resources, thus adversely affecting wheat yield (Cavanagh et al, 2013 ; Sthapit et al, 2020 ). Notably, numerous genetic resources for agronomic traits and disease resistance from wheat-related species may effectively solve future wheat production challenges (Zaïm et al, 2017 ; El Haddad et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat (Triticum turgidum L.) Population: Chinese Landrace “Ailanmai” × Wild Emmer

Zhu

Wei

et al. 2021

Front. Plant Sci.

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Spikelet number per spike (SNS) is the primary factor that determines wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace “Ailanmai” × wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using a wheat 55K single- nucleotide polymorphism (SNP) array. The linkage map containing 1,150 bin markers with a total genetic distance of 2,411.8 cm was obtained. Based on the phenotypic data from the eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTLs) for SNS were identified, explaining 6.71–29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.2 and QSns.sau-AM-3B.2, were detected as a major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked kompetitive allele-specific PCR (KASP) markers. Potential candidate genes within the physical intervals of the corresponding QTLs were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of the wheat 55K SNP array developed for common wheat in the genetic mapping of tetraploid population and shows the potential application of wheat-related species in wheat improvement programs.

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“…Given its important role in yield formation, more loci for SNS should be identi ed and utilized. However, modern wheat breeding reduces the genetic diversity among cultivars and narrows the genetic basis of common wheat leading to a detrimental effect on future wheat improvement [12][13][14]. Fortunately, a great quantity of undeveloped genetic resources from wheat related species may effectively meet the challenges of future wheat production [15][16][17].…”

Section: Introductionmentioning

confidence: 99%

The Wheat 55K SNP-Based Exploration of Loci for Spikelet Number Per Spike From a Tetraploid Wheat (Triticum Turgidum L.) Recombinant Inbred Line Population Derived From a Chinese Landrace ‘ailanmai’ and a Wild Emmer Accession

Zhu

Wei

et al. 2020

Preprint

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Background: Increasing wheat yield is an urgent task to solve the global food shortage. Spikelet number per spike (SNS) is a key factor in determining kernel number per spike which has a great effect on wheat grain yield. However, modern wheat breeding narrows genetic diversity among cultivars leading to a detrimental effect on future wheat improvement. It is thus of great significance to explore new genetic resources for SNS to increase wheat yield.Results: A tetraploid landrace ‘Ailanmai’ × wild emmer wheat recombinant inbred line (RIL) population was used to construct a high-density genetic map using the wheat 55K single nucleotide polymorphism (SNP) array. The results showed that 94.83% (6204) of the mapped markers had consistent genetic and physical chromosomal locations. Subsequently, fourteen quantitative trait loci (QTL) for SNS explaining 4.23-27.26% of the phenotypic variation were identified. QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2 were considered as major and novel QTL and their combination had the largest effect and increased SNS by 17.47%. In the physical intervals of QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2, some development-related genes were predicted to participate in the spikelet growth and affect SNS. Additionally, significant correlations between SNS and other agronomic traits like significant and positive correlation between SNS and thousand kernel weight were detected and analyzed. Conclusions: Our study demonstrated the feasibility of wheat 55K SNP array in genetic mapping of tetraploid wheat and provided an example of exploring outstanding genetic resources from wheat related species for further utilization in common wheat improvement.

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Genetic diversity in historical and modern wheat varieties of the U.S. Pacific Northwest

Cited by 14 publications

References 49 publications

Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array

Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array

The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat (Triticum turgidum L.) Population: Chinese Landrace “Ailanmai” × Wild Emmer

The Wheat 55K SNP-Based Exploration of Loci for Spikelet Number Per Spike From a Tetraploid Wheat (Triticum Turgidum L.) Recombinant Inbred Line Population Derived From a Chinese Landrace ‘ailanmai’ and a Wild Emmer Accession

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