scholarly journals Genome-wide association study for morphological, phenological, quality, and yield traits in einkorn (Triticum monococcum L. subsp. monococcum)

2021 ◽  
Author(s):  
Andrea Volante ◽  
Delfina Barabaschi ◽  
Rosanna Marino ◽  
Andrea Brandolini
Keyword(s):  
Association Mapping ◽  
Bronze Age ◽  
Bread Wheat ◽  
Genome Wide Association Study ◽  
Triticum Monococcum ◽  
Distribution Area ◽  
Phenotypic Traits ◽  
European Area ◽  
A Genome ◽  
Starting Point

Abstract Einkorn (Triticum monococcum L. subsp. monococcum, 2n = 2× = 14, AmAm) is a diploid wheat whose cultivation was widespread in the Mediterranean and European area till the Bronze Age, before it was replaced by the more productive durum and bread wheats. Although scarcely cultivated nowadays, it has gained renewed interest due to its relevant nutritional properties and as source of genetic diversity for crop breeding. However, the molecular basis of many traits of interest in einkorn remain still unknown. A panel of 160 einkorn landraces, from different parts of the distribution area, was characterized for several phenotypic traits related to morphology, phenology, quality, and yield for 4 years in two locations. An approach based on co-linearity with the A genome of bread wheat, supported also by that with Triticum urartu genome, was exploited to perform association mapping, even without an einkorn anchored genome. The association mapping approach uncovered numerous marker-trait associations; for 37 of these, a physical position was inferred by homology with the bread wheat genome. Moreover, numerous associated regions were also assigned to the available T. monococcum contigs. Among the intervals detected in this work, three overlapped with regions previously described as involved in the same trait, while four other regions were localized in proximity of loci previously described and presumably refer to the same gene/QTL. The remaining associated regions identified in this work could represent a novel and useful starting point for breeding approaches to improve the investigated traits in this neglected species.

scholarly journals Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 493
Author(s):  
Salvatore Mastrangelo ◽  
Filippo Cendron ◽  
Gianluca Sottile ◽  
Giovanni Niero ◽  
Baldassare Portolano ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Snp Array ◽  
Fixation Index ◽  
Phenotypic Traits ◽  
Plumage Color ◽  
Phenotypic Marker ◽  
Genome Wide ◽  
A Genome ◽  
The Difference ◽  
Genomic Regions

Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (FST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and FST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken.

scholarly journals Genome-wide association for heifer reproduction and calf performance traits in beef cattle

Genome ◽  
2015 ◽  
Vol 58 (12) ◽  
pp. 549-557 ◽  
Author(s):  
Everestus C. Akanno ◽  
Graham Plastow ◽  
Carolyn Fitzsimmons ◽  
Stephen P. Miller ◽  
Vern Baron ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Genome Wide Association Study ◽  
Average Daily Gain ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Research Centre ◽  
Genome Wide ◽  
A Genome ◽  
Starting Point ◽  
And Performance

The aim of this study was to identify SNP markers that associate with variation in beef heifer reproduction and performance of their calves. A genome-wide association study was performed by means of the generalized quasi-likelihood score (GQLS) method using heifer genotypes from the BovineSNP50 BeadChip and estimated breeding values for pre-breeding body weight (PBW), pregnancy rate (PR), calving difficulty (CD), age at first calving (AFC), calf birth weight (BWT), calf weaning weight (WWT), and calf pre-weaning average daily gain (ADG). Data consisted of 785 replacement heifers from three Canadian research herds, namely Brandon Research Centre, Brandon, Manitoba, University of Alberta Roy Berg Kinsella Ranch, Kinsella, Alberta, and Lacombe Research Centre, Lacombe, Alberta. After applying a false discovery rate correction at a 5% significance level, a total of 4, 3, 3, 9, 6, 2, and 1 SNPs were significantly associated with PBW, PR, CD, AFC, BWT, WWT, and ADG, respectively. These SNPs were located on chromosomes 1, 5–7, 9, 13–16, 19–21, 24, 25, and 27–29. Chromosomes 1, 5, and 24 had SNPs with pleiotropic effects. New significant SNPs that impact functional traits were detected, many of which have not been previously reported. The results of this study support quantitative genetic studies related to the inheritance of these traits, and provides new knowledge regarding beef cattle quantitative trait loci effects. The identification of these SNPs provides a starting point to identify genes affecting heifer reproduction traits and performance of their calves (BWT, WWT, and ADG). They also contribute to a better understanding of the biology underlying these traits and will be potentially useful in marker- and genome-assisted selection and management.

scholarly journals Genome-Wide Association Mapping for Heat and Drought Adaptive Traits in Pea

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1897
Author(s):  
Endale G. Tafesse ◽  
Krishna K. Gali ◽  
V. B. Reddy Lachagari ◽  
Rosalind Bueckert ◽  
Thomas D. Warkentin
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Vegetation Index ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Adaptive Traits ◽  
Flowering Duration ◽  
Genome Wide ◽  
A Genome

Heat and drought, individually or in combination, limit pea productivity. Fortunately, substantial genetic diversity exists in pea germplasm for traits related to abiotic stress resistance. Understanding the genetic basis of resistance could accelerate the development of stress-adaptive cultivars. We conducted a genome-wide association study (GWAS) in pea on six stress-adaptive traits with the aim to detect the genetic regions controlling these traits. One hundred and thirty-five genetically diverse pea accessions were phenotyped in field studies across three or five environments under stress and control conditions. To determine marker trait associations (MTAs), a total of 16,877 valuable single nucleotide polymorphisms (SNPs) were used in association analysis. Association mapping detected 15 MTAs that were significantly (p ≤ 0.0005) associated with the six stress-adaptive traits averaged across all environments and consistent in multiple individual environments. The identified MTAs were four for lamina wax, three for petiole wax, three for stem thickness, two for the flowering duration, one for the normalized difference vegetation index (NDVI), and two for the normalized pigment and chlorophyll index (NPCI). Sixteen candidate genes were identified within a 15 kb distance from either side of the markers. The detected MTAs and candidate genes have prospective use towards selecting stress-hardy pea cultivars in marker-assisted selection.

scholarly journals Exploring the Genetic Architecture of Root-Related Traits in Mediterranean Bread Wheat Landraces by Genome-Wide Association Analysis

Agronomy ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 613 ◽  
Author(s):  
Rubén Rufo ◽  
Silvio Salvi ◽  
Conxita Royo ◽  
Jose Soriano
Keyword(s):  
Molecular Markers ◽  
Bread Wheat ◽  
Root Development ◽  
Genome Wide Association Study ◽  
Abiotic Stress Tolerance ◽  
Genome Wide Association ◽  
Mediterranean Countries ◽  
Genome Wide ◽  
A Genome ◽  
Wheat Landraces

Background: Roots are essential for drought adaptation because of their involvement in water and nutrient uptake. As the study of the root system architecture (RSA) is costly and time-consuming, it is not generally considered in breeding programs. Thus, the identification of molecular markers linked to RSA traits is of special interest to the breeding community. The reported correlation between the RSA of seedlings and adult plants simplifies its assessment. Methods: In this study, a panel of 170 bread wheat landraces from 24 Mediterranean countries was used to identify molecular markers associated with the seminal RSA and related traits: seminal root angle, total root number, root dry weight, seed weight and shoot length, and grain yield (GY). Results: A genome-wide association study identified 135 marker-trait associations explaining 6% to 15% of the phenotypic variances for root related traits and 112 for GY. Fifteen QTL hotspots were identified as the most important for controlling root trait variation and were shown to include 31 candidate genes related to RSA traits, seed size, root development, and abiotic stress tolerance (mainly drought). Co-location for root related traits and GY was found in 17 genome regions. In addition, only four out of the fifteen QTL hotspots were reported previously. Conclusions: The variability found in the Mediterranean wheat landraces is a valuable source of root traits to introgress into adapted phenotypes through marker-assisted breeding. The study reveals new loci affecting root development in wheat.

scholarly journals Identification of Quantitative Trait Loci for Leaf Rust and Stem Rust Seedling Resistance in Bread Wheat Using a Genome-Wide Association Study

Plants ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 74
Author(s):  
Alibek Zatybekov ◽  
Yuliya Genievskaya ◽  
Aralbek Rsaliyev ◽  
Akerke Maulenbay ◽  
Gulbahar Yskakova ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Association Study ◽  
Leaf Rust ◽  
Bread Wheat ◽  
Stem Rust ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

In recent years, leaf rust (LR) and stem rust (SR) have become a serious threat to bread wheat production in Kazakhstan. Most local cultivars are susceptible to these rusts, which has affected their yield and quality. The development of new cultivars with high productivity and LR and SR disease resistance, including using marker-assisted selection, is becoming an important priority in local breeding projects. Therefore, the search for key genetic factors controlling resistance in all plant stages, including the seedling stage, is of great significance. In this work, we applied a genome-wide association study (GWAS) approach using 212 local bread wheat accessions that were phenotyped for resistance to specific races of Puccinia triticina Eriks. (Pt) and Puccinia graminis f. sp. tritici (Pgt) at the seedling stages. The collection was genotyped using a 20 K Illumina iSelect SNP assay, and 11,150 polymorphic SNP markers were selected for the association mapping. Using a mixed linear model, we identified 11 quantitative trait loci (QTLs) for five out of six specific races of Pt and Pgt. The comparison of the results from this GWAS with those from previously published work showed that nine out of eleven QTLs for LR and SR resistance had been previously reported in a GWAS study at the adult plant stages of wheat growth. Therefore, it was assumed that these nine common identified QTLs were effective for all-stage resistance to LR and SR, and the two other QTLs appear to be novel QTLs. In addition, five out of these nine QTLs that had been identified earlier were found to be associated with yield components, suggesting that they may directly influence the field performance of bread wheat. The identified QTLs, including novel QTLs found in this study, may play an essential role in the breeding process for improving wheat resistance to LR and SR.

scholarly journals The Genomic Architecture of Competitive Response of Arabidopsis thaliana Is Highly Flexible Among Plurispecific Neighborhoods

2021 ◽  
Vol 12 ◽  
Author(s):  
Cyril Libourel ◽  
Etienne Baron ◽  
Juliana Lenglet ◽  
Laurent Amsellem ◽  
Dominique Roby ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Species ◽  
Stress Responses ◽  
Genome Wide Association Study ◽  
Species Assemblages ◽  
Phenotypic Traits ◽  
Limited Information ◽  
Competitive Response ◽  
Stellaria Media ◽  
A Genome

Plants are daily challenged by multiple abiotic and biotic stresses. A major biotic constraint corresponds to competition with other plant species. Although plants simultaneously interact with multiple neighboring species throughout their life cycle, there is still very limited information about the genetics of the competitive response in the context of plurispecific interactions. Using a local mapping population of Arabidopsis thaliana, we set up a genome wide association study (GWAS) to estimate the extent of genetic variation of competitive response in 12 plant species assemblages, based on three competitor species (Poa annua, Stellaria media, and Veronica arvensis). Based on five phenotypic traits, we detected strong crossing reaction norms not only between the three bispecific neighborhoods but also among the plurispecific neighborhoods. The genetic architecture of competitive response was highly dependent on the identity and the relative abundance of the neighboring species. In addition, most of the enriched biological processes underlying competitive responses largely differ among neighborhoods. While the RNA related processes might confer a broad range response toolkit for multiple traits in diverse neighborhoods, some processes, such as signaling and transport, might play a specific role in particular assemblages. Altogether, our results suggest that plants can integrate and respond to different species assemblages depending on the identity and number of each neighboring species, through a large range of candidate genes associated with diverse and unexpected processes leading to developmental and stress responses.

scholarly journals Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Şakir Burak Bükücü ◽  
Mehmet Sütyemez ◽  
Sina Kefayati ◽  
Aibibula Paizila ◽  
Abdulqader Jighly ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Juglans Regia ◽  
Genotypic Variation ◽  
Phenotypic Traits ◽  
Juvenile Period ◽  
Phenotypic Data ◽  
Breeding Programs ◽  
Genome Wide ◽  
A Genome ◽  
Major Qtl

Abstract Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R2 between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits in Juglans regia L. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.

scholarly journals The genomic architecture of competitive response of Arabidopsis thaliana is highly flexible between monospecific and plurispecific neighborhoods

2019 ◽  
Author(s):  
Cyril Libourel ◽  
Etienne Baron ◽  
Juliana Lenglet ◽  
Laurent Amsellem ◽  
Dominique Roby ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Stress Responses ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Species Assemblages ◽  
Phenotypic Traits ◽  
Limited Information ◽  
Competitive Response ◽  
A Genome ◽  
Set Up

AbstractAlthough plants simultaneously interact with multiple neighboring species throughout their life cycle, there is still very limited information about the genetics of the competitive response in the context of plurispecific interactions. Using a local mapping population of Arabidopsis thaliana, we set up a Genome Wide Association study to estimate the extent of genetic variation of the competitive response in presence of 12 plant species assemblages, and to compare the genetic architecture of the competitive response between monospecific and plurispecific neighborhoods. Based on four phenotypic traits, we detected strong crossing reaction norms not only among the three monospecific neighborhoods, but also among the different plant assemblages. Accordingly, the genetic architecture of the competitive response was highly dependent on the identity and the relative abundance of the neighboring species. In addition, enriched biological processes underlying the competitive response largely differ between monospecific and plurispecific neighborhoods. In particular, receptor-like kinases and transporters were significantly enriched in plurispecific neighborhoods. Our results suggest that plants can integrate and respond to different species assemblages depending on the identity and number of each neighboring species, through a large range of genes associated mainly with perception and signaling processes leading to developmental and stress responses.

scholarly journals Genome-wide association study for anther length in some elite bread wheat germplasm

2018 ◽  
Vol 54 (No. 3) ◽  
pp. 109-114 ◽  
Author(s):  
Song Xiaopeng ◽  
Feng Jie ◽  
Cui Zixia ◽  
Zhang Chuanliang ◽  
Sun Daojie
Keyword(s):  
Association Study ◽  
Bread Wheat ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Pollen Grains ◽  
Triticum Aestivum L ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Anther Length ◽  
A Genome

The anther is a crucial organ for the development of the spike in bread wheat (Triticum aestivum L.). Long anthers contain large amounts of pollen grains; thus, they are favourable for cross-pollination and increase resilience against adverse environmental conditions. We conducted a genome-wide association study (GWAS) of anther length in 305 elite wheat lines evaluated during 2013–2015 in two locations and two growing seasons. The mapping panel was genotyped using a high-density Illumina iSelect 90K single nucleotide polymorphism (SNP) array. The GWAS used 18763 SNPs and identified 17 markers associated with anther length in wheat. The loci were mainly distributed across the chromosomes 3A, 3B and 7B. Further studies are required to determine if these are candidate genomic regions of anther length. In addition, anther length had high heritability, and positive correlations between anther length and grain weight per spike were observed.  

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