Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding

Liu, Jindong; Rasheed, Awais; He, Zhonghu; Imtiaz, Muhammad; Arif, Anjuman; Mahmood, Tariq; Ghafoor, Abdul; Siddiqui, Sadar Uddin; Ilyas, Muhammad; Wen, Weie; Gao, Fengjie; Xie, Chaojie; Xia, Xianchun

doi:10.1007/s00122-019-03367-4

Cited by 39 publications

(41 citation statements)

References 83 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…More recently, Zhou et al [57] found 148 selective regions in a collection of 717 Chinese wheat landraces associated with yield and disease resistance. Liu et al [15], using a worldwide panel comprising landraces from China and Pakistan and modern cultivars genotyped with the 90K SNP array, identified 477 selective sweeps. Some of these loci comprised known functional genes for disease resistance, vernalization, quality, adaptability, and yield.…”

Section: Detection Of Selective Sweeps By Eigengwasmentioning

confidence: 99%

See 1 more Smart Citation

Labelling Selective Sweeps Used in Durum Wheat Breeding from a Diverse and Structured Panel of Landraces and Cultivars

Soriano

Sansaloni

Ammar

et al. 2021

Biology

View full text Add to dashboard Cite

A panel of 387 durum wheat genotypes including Mediterranean landraces and modern cultivars was characterized with 46,161 diversity arrays technology (DArTseq) markers. Analysis of population structure uncovered the existence of five subpopulations (SP) related to the pattern of migration of durum wheat from the domestication area to the west of the Mediterranean basin (SPs 1, 2, and 3) and further improved germplasm (SPs 4 and 5). The total genetic diversity (HT) was 0.40 with a genetic differentiation (GST) of 0.08 and a mean gene flow among SPs of 6.02. The lowest gene flow was detected between SP 1 (presumably the ancient genetic pool of the panel) and SPs 4 and 5. However, gene flow from SP 2 to modern cultivars was much higher. The highest gene flow was detected between SP 3 (western Mediterranean germplasm) and SP 5 (North American and European cultivars). A genome wide association study (GWAS) approach using the top ten eigenvectors as phenotypic data revealed the presence of 89 selective sweeps, represented as quantitative trait loci (QTL) hotspots, widely distributed across the durum wheat genome. A principal component analysis (PCoA) using 147 markers with −log10 p >5 identified three regions located on chromosomes 2A, 2B and 3A as the main drivers for differentiation of Mediterranean landraces. Gene flow between SPs offers clues regarding the putative use of Mediterranean old durum germplasm by the breeding programs represented in the structure analysis. EigenGWAS identified selective sweeps among landraces and modern cultivars. The analysis of the corresponding genomic regions in the ‘Zavitan’, ‘Svevo’ and ‘Chinese Spring’ genomes discovered the presence of important functional genes including Ppd, Vrn, Rht, and gene models involved in important biological processes including LRR-RLK, MADS-box, NAC, and F-box.

show abstract

Section: Detection Of Selective Sweeps By Eigengwasmentioning

confidence: 99%

“…EigenGWAS has been successfully applied in crop species such as maize [14], wheat [15], and barley [16].…”

Section: Introductionmentioning

confidence: 99%

Labelling Selective Sweeps Used in Durum Wheat Breeding from a Diverse and Structured Panel of Landraces and Cultivars

Soriano

Sansaloni

Ammar

et al. 2021

Biology

View full text Add to dashboard Cite

show abstract

“…For wheat, where marker number and density were major lacunae in conducting in-depth genetic analyses, the availability of dense sets of single-nucleotide polymorphisms (SNPs) from different genotyping platforms has made a powerful step change in the marker tool kit (Poland et al, 2012;Cavanagh et al, 2013;Wang et al, 2014). The resulting high-density genomic data have opened up new possibilities for untangling the genetic architecture of complex traits by genome-wide association study (GWAS) and to perform other genomic studies, for instance, the analysis of selective sweeps within or across species (Afzal et al, 2019;Liu et al, 2019). Additionally, the recent availability of the high-quality reference genome of bread wheat (IWGSC, 2018) has enhanced our understanding of the regulation of genome organization, gene expression, and evolutionary mechanisms shaping its genome (Alaux et al, 2018;Ramírez-González et al, 2018;Wicker et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Haplotype-Based, Genome-Wide Association Study Reveals Stable Genomic Regions for Grain Yield in CIMMYT Spring Bread Wheat

et al. 2020

View full text Add to dashboard Cite

We untangled key regions of the genetic architecture of grain yield (GY) in CIMMYT spring bread wheat by conducting a haplotype-based, genome-wide association study (GWAS), together with an investigation of epistatic interactions using seven large sets of elite yield trials (EYTs) consisting of a total of 6,461 advanced breeding lines. These lines were phenotyped under irrigated and stress environments in seven growing seasons (2011–2018) and genotyped with genotyping-by-sequencing markers. Genome-wide 519 haplotype blocks were constructed, using a linkage disequilibrium-based approach covering 14,036 Mb in the wheat genome. Haplotype-based GWAS identified 7, 4, 10, and 15 stable (significant in three or more EYTs) associations in irrigated (I), mild drought (MD), severe drought (SD), and heat stress (HS) testing environments, respectively. Considering all EYTs and the four testing environments together, 30 stable associations were deciphered with seven hotspots identified on chromosomes 1A, 1B, 2B, 4A, 5B, 6B, and 7B, where multiple haplotype blocks were associated with GY. Epistatic interactions contributed significantly to the genetic architecture of GY, explaining variation of 3.5–21.1%, 3.7–14.7%, 3.5–20.6%, and 4.4– 23.1% in I, MD, SD, and HS environments, respectively. Our results revealed the intricate genetic architecture of GY, controlled by both main and epistatic effects. The importance of these results for practical applications in the CIMMYT breeding program is discussed.

show abstract

“…Cultivated wheat is the second most important food crop, providing calories and nutrients for up to one third of the world population. Before the Green Revolution, wheat was cultivated mainly (with few exceptions) as landraces [ 1 , 2 ]. Local landraces (e.g., Banatka, Beloturka, Poltavka, Kubanka, Arnautka, and others for the former USSR) were more heterogeneous in genetic composition, which had a number of advantages: greater plasticity of the genomes that make up their high adaptivity to local conditions and tolerance to abiotic stress [ 3 , 4 , 5 ].…”

Section: Introductionmentioning

confidence: 99%

“…However, as a result of modern breeding, most landraces were replaced by high-yielding disease, and lodging resistant (but genetically homogeneous) cultivars. As a result, the genetic diversity of wheat shifted towards European germplasm, especially in Asian countries, and was accompanied by the loss of the local old varieties [ 2 , 5 , 6 , 7 ]. The introgression of agronomically valuable traits from the Triticeae wild species via wide hybridization has been proved to be one of the efficient tools to enrich wheat gene repertoire [ 6 , 8 , 9 ].…”

Section: Introductionmentioning

confidence: 99%

Development of Specific Thinopyrum Cytogenetic Markers for Wheat-Wheatgrass Hybrids Using Sequencing and qPCR Data

Nikitina

Kuznetsova

Kroupin

et al. 2020

IJMS

View full text Add to dashboard Cite

The cytogenetic study of wide hybrids of wheat has both practical and fundamental values. Partial wheat-wheatgrass hybrids (WWGHs) are interesting as a breeding bridge to confer valuable genes to wheat genome, as well as a model object that contains related genomes of Triticeae. The development of cytogenetic markers is a process that requires long and laborious fluorescence in situ hybridization (FISH) testing of various probes before a suitable probe is found. In this study, we aimed to find an approach that allows to facilitate this process. Based on the data sequencing of Thinopyrum ponticum, we selected six tandem repeat (TR) clusters using RepeatExplorer2 pipeline and designed primers for each of them. We estimated the found TRs’ abundance in the genomes of Triticum aestivum, Thinopyrum ponticum, Thinopyrum intermedium and four different WWGH accessions using real-time qPCR, and localized them on the chromosomes of the studied WWGHs using fluorescence in situ hybridization. As a result, we obtained three tandem repeat cytogenetic markers that specifically labeled wheatgrass chromosomes in the presence of bread wheat chromosomes. Moreover, we designed and tested primers for these repeats, and demonstrated that they can be used as qPCR markers for quick and cheap monitoring of the presence of certain chromosomes of wheatgrass in breeding programs.

show abstract

Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding

Cited by 39 publications

References 83 publications

Labelling Selective Sweeps Used in Durum Wheat Breeding from a Diverse and Structured Panel of Landraces and Cultivars

Labelling Selective Sweeps Used in Durum Wheat Breeding from a Diverse and Structured Panel of Landraces and Cultivars

Haplotype-Based, Genome-Wide Association Study Reveals Stable Genomic Regions for Grain Yield in CIMMYT Spring Bread Wheat

Development of Specific Thinopyrum Cytogenetic Markers for Wheat-Wheatgrass Hybrids Using Sequencing and qPCR Data

Contact Info

Product

Resources

About