Geographical comparison of genetic diversity in Asian landrace wheat (Triticum aestivum L.) germplasm based on high-molecular-weight glutenin subunits

Lee, Sukyeung; Choi, Yu-Mi; Lee, Myung Chul; Hyun, Do Yoon; Oh, Sejong; Jung, Yongju

doi:10.1007/s10722-018-0633-6

Cited by 9 publications

(7 citation statements)

References 38 publications

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“…Furthermore, the high levels of overall admixture between the landraces as revealed by all the methods used in the study may also be attributed to the free exchange of seeds between farmers of the north-eastern states of Afghanistan. This is in agreement with previous studies reporting high admixture and low genetic variation among the Afghan landraces [5,42,43]. A previous study of the population structure and genetic diversity of diverse 446 Afghan landraces collected from 17 provinces and different agro-climatic regions showed higher genetic diversity compared with our study [2].…”

Section: Population Structuresupporting

confidence: 93%

Genetic Diversity and Population Structure Analysis of Triticum aestivum L. Landrace Panel from Afghanistan

Tehseen

Iştipliler

Kehel³

et al. 2021

Genes

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Landraces are a potential source of genetic diversity and provide useful genetic resources to cope with the current and future challenges in crop breeding. Afghanistan is located close to the centre of origin of hexaploid wheat. Therefore, understanding the population structure and genetic diversity of Afghan wheat landraces is of enormous importance in breeding programmes for the development of high-yielding cultivars as well as broadening the genetic base of bread wheat. Here, a panel of 363 bread wheat landraces collected from seven north and north-eastern provinces of Afghanistan were evaluated for population structure and genetic diversity using single nucleotide polymorphic markers (SNPs). The genotyping-by-sequencing of studied landraces after quality control provided 4897 high-quality SNPs distributed across the genomes A (33.75%), B (38.73%), and D (27.50%). The population structure analysis was carried out by two methods using model-based STRUCTURE analysis and cluster-based discriminant analysis of principal components (DAPC). The analysis of molecular variance showed a higher proportion of variation within the sub-populations compared with the variation observed as a whole between sub-populations. STRUCTURE and DAPC analysis grouped the majority of the landraces from Badakhshan and Takhar together in one cluster and the landraces from Baghlan and Kunduz in a second cluster, which is in accordance with the micro-climatic conditions prevalent within the north-eastern agro-ecological zone. Genetic distance analysis was also studied to identify differences among the Afghan regions; the strongest correlation was observed for the Badakhshan and Takhar (0.003), whereas Samangan and Konarha (0.399) showed the highest genetic distance. The population structure and genetic diversity analysis highlighted the complex genetic variation present in the landraces which were highly correlated to the geographic origin and micro-climatic conditions within the agro-climatic zones of the landraces. The higher proportions of admixture could be attributed to historical unsupervised exchanges of seeds between the farmers of the central and north-eastern provinces of Afghanistan. The results of this study will provide useful information for genetic improvement in wheat and is essential for association mapping and genomic prediction studies to identify novel sources for resistance to abiotic and biotic stresses.

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Section: Population Structuresupporting

confidence: 93%

Genetic Diversity and Population Structure Analysis of Triticum aestivum L. Landrace Panel from Afghanistan

Tehseen

Iştipliler

Kehel³

et al. 2021

Genes

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“… Chen et al (2019) reported that the landraces from Western Asia (Turkey, Syria, Iran, and Iraq) were clustered together and also showed a degree of admixture within the two major clusters identified which separated the landraces from this region from the rest of the landraces and cultivars of other regions. A study of 1,068 wheat landraces from East Asia and West Asia divided the panel into three main subpopulations, interestingly Syrian and Turkish landraces were clustered together, whereas the Iranian landraces showed more genetic similarity with the Afghan landraces than the Syrian and Turkish ones ( Lee et al, 2018 ). The Fertile Crescent which includes modern-day Turkey and Syria is considered the center of origin of the wheat crop, which explains the complex background and admixture present among the landraces collected from these countries ( Karagöz, 2014 ; Baloch et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

Exploring the Genetic Diversity and Population Structure of Wheat Landrace Population Conserved at ICARDA Genebank

et al. 2022

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Landraces are considered a valuable source of potential genetic diversity that could be used in the selection process in any plant breeding program. Here, we assembled a population of 600 bread wheat landraces collected from eight different countries, conserved at the ICARDA's genebank, and evaluated the genetic diversity and the population structure of the landraces using single nucleotide polymorphism (SNP) markers. A total of 11,830 high-quality SNPs distributed across the genomes A (40.5%), B (45.9%), and D (13.6%) were used for the final analysis. The population structure analysis was evaluated using the model-based method (STRUCTURE) and distance-based methods [discriminant analysis of principal components (DAPC) and principal component analysis (PCA)]. The STRUCTURE method grouped the landraces into two major clusters, with the landraces from Syria and Turkey forming two clusters with high proportions of admixture, whereas the DAPC and PCA analysis grouped the population into three subpopulations mostly according to the geographical information of the landraces, i.e., Syria, Iran, and Turkey with admixture. The analysis of molecular variance revealed that the majority of the variation was due to genetic differences within the populations as compared with between subpopulations, and it was the same for both the cluster-based and distance-based methods. Genetic distance analysis was also studied to estimate the differences between the landraces from different countries, and it was observed that the maximum genetic distance (0.389) was between the landraces from Spain and Palestine, whereas the minimum genetic distance (0.013) was observed between the landraces from Syria and Turkey. It was concluded from the study that the model-based methods (DAPC and PCA) could dissect the population structure more precisely when compared with the STRUCTURE method. The population structure and genetic diversity analysis of the bread wheat landraces presented here highlight the complex genetic architecture of the landraces native to the Fertile Crescent region. The results of this study provide useful information for the genetic improvement of hexaploid wheat and facilitate the use of landraces in wheat breeding programs.

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“… Chen et al (2019) described that West Asian, European, numerous Central and South Asian landraces, and most East Asian cultivars grouped in the same cluster, whiles most of the East Asian landraces were grouped with South, Central and West Asian landraces. Lee et al (2018) described that most Japanese, Korean and genotypes from Afghanistan were grouped in a cluster, while the Middle Eastern, Chinese, and Caucasus germplasm were in a separate group. The genetic diversity and population structure in the current ABLs were not surprising since the genetic composition, despite being variable, is restricted due to common ancestry ( Table S1 ), leading to closely linked clusters.…”

Section: Discussionmentioning

confidence: 99%

Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)

Tomar

Dhillon

Singh

et al. 2021

PeerJ

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Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.

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Geographical comparison of genetic diversity in Asian landrace wheat (Triticum aestivum L.) germplasm based on high-molecular-weight glutenin subunits

Cited by 9 publications

References 38 publications

Genetic Diversity and Population Structure Analysis of Triticum aestivum L. Landrace Panel from Afghanistan

Genetic Diversity and Population Structure Analysis of Triticum aestivum L. Landrace Panel from Afghanistan

Exploring the Genetic Diversity and Population Structure of Wheat Landrace Population Conserved at ICARDA Genebank

Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)

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