Application of marker-assisted selection and genome-wide association scanning to the development of winter food barley germplasm resources

100-seed weight (100-SW) in soybeans is a yield component trait and controlled by multiple genes with different effects, but limited information is available for its quantitative trait nucleotides (QTNs) and candidate genes. To better understand the genetic architecture underlying the trait and improve the precision of marker-assisted selection, a total of 43,834 single nucleotide polymorphisms (SNPs) in 250 soybean accessions were used to identify significant QTNs for 100-SW in four environments and their BLUP values using six multi-locus and one single-locus genome-wide association study methods. As a result, a total of 218 significant QTNs were detected using multi-locus methods, whereas eight QTNs were identified by a single-locus method. Among 43 QTNs or QTN clusters identified repeatedly across various environments and/or approaches, all of them exhibited significant trait differences between their corresponding alleles, 33 were found in the genomic region of previously reported QTLs, 10 were identified as new QTNs, and three (qHSW-4-1, qcHSW-7-3, and qcHSW-10-4) were detected in all the four environments. The number of seed weight (SW) increasing alleles for each accession ranged from 8 (18.6%) to 36 (83.72%), and three accessions (Yixingwuhuangdou, Nannong 95C-5, and Yafanzaodou) had more than 35 SW increasing alleles. Among 36 homologous seed-weight genes in Arabidopsis underlying the above 43 stable QTNs, more importantly, Glyma05g34120, GmCRY1, and GmCPK11 had known seed-size/weight-related genes in soybean, and Glyma07g07850, Glyma10g03440, and Glyma10g36070 were candidate genes identified in this study. These results provide useful information for genetic foundation, marker-assisted selection, genomic prediction, and functional genomics of 100-SW.

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Genome-Wide Association Mapping of Malting Quality Traits in Relevant Barley Germplasm in Uruguay

Advance in Barley Sciences ◽

10.1007/978-94-007-4682-4_3 ◽

2012 ◽

pp. 37-46 ◽

Cited By ~ 2

Author(s):

Ariel Castro ◽

Lorena Cammarota ◽

Blanca Gomez ◽

Lucia Gutierrez ◽

Patrick M. Hayes ◽

...

Keyword(s):

Association Mapping ◽

Genome Wide Association ◽

Malting Quality ◽

Quality Traits ◽

Genome Wide ◽

Barley Germplasm

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Genome-Wide Association Analysis of Late Blight Resistance Traits in Potato Germplasm Resources

10.21203/rs.3.rs-113697/v1 ◽

2020 ◽

Author(s):

Fang Wang ◽

Meiling Zou ◽

Long Zhao ◽

Huaqing Li ◽

Zhiqiang Xia ◽

...

Keyword(s):

Late Blight ◽

Candidate Genes ◽

Association Analysis ◽

Late Blight Resistance ◽

Genome Wide Association ◽

Blight Resistance ◽

Germplasm Resources ◽

Potato Germplasm ◽

Genome Wide ◽

Population Structure Analysis

Abstract Background: Potatoes are dicotyledonous plants of the genus Solanum, family Solanaceae, and contain large amounts of starch, proteins, and trace elements required by the human. Potato late blight is the main disease hindering potato production. In this study, Phytophthora infestans were used to quantify late blight resistance in 284 germplasm resources, and resistance genes were mined through genome-wide association analysis.Results: The results showed that among the 284 potato germplasm resources, 37 showed immunity, 15 were highly resistant to late blight, 30 were moderately resistant to late blight, 107 were moderately susceptible to late blight, and 95 were highly susceptible to late blight. Through screening and filtering, 22,489 high-quality single-nucleotide polymorphisms (SNPs) and indels were obtained. Through population structure analysis and principal-component analysis, 284 germplasm resources were divided into eight subgroups, which was consistent with the results of the phylogenetic tree analysis. The genetic diversity index of the 284 potato germplasm resources was 0.2161, and the differentiation index of each subgroup was 0.0251-0.1489. A mixed linear model was built to perform an association analysis on the diameter of the lesions identified from isolated leaves of potato affected by late blight. The genes within 100 kb of both sides of the obtained significant SNP loci were searched and functionally annotated, and 18 candidate genes were obtained. Twenty-two candidate genes were obtained from the association analysis of disease resistance grade.Conclusions: 284 potato germplasm resources were used to identify for Phytophthora infestans resistance. The potato germplasm resources were divided into 8 subgroups by population structure analysis, and the main differentiation among subgroups was moderate. Candidate genes were mined by genome-wide association analysis.The results of this study provides the foundation for the genetic improvement of potato varieties resistant to late blight.

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Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan

PeerJ ◽

10.7717/peerj.11857 ◽

2021 ◽

Vol 9 ◽

pp. e11857

Author(s):

Akerke Amalova ◽

Saule Abugalieva ◽

Adylkhan Babkenov ◽

Sandukash Babkenova ◽

Yerlan Turuspekov

Keyword(s):

Association Study ◽

Spring Wheat ◽

Marker Assisted Selection ◽

Genome Wide Association Study ◽

Snp Markers ◽

Genome Wide Association ◽

Northern Kazakhstan ◽

Genome Wide ◽

Rainfed Conditions ◽

Selection Approach

Background Bread wheat is the most important cereal in Kazakhstan, where it is grown on over 12 million hectares. One of the major constraints affecting wheat grain yield is drought due to the limited water supply. Hence, the development of drought-resistant cultivars is critical for ensuring food security in this country. Therefore, identifying quantitative trait loci (QTLs) associated with drought tolerance as an essential step in modern breeding activities, which rely on a marker-assisted selection approach. Methods A collection of 179 spring wheat accessions was tested under irrigated and rainfed conditions in Northern Kazakhstan over three years (2018, 2019, and 2020), during which data was collected on nine traits: heading date (HD), seed maturity date (SMD), plant height (PH), peduncle length (PL), number of productive spikes (NPS), spike length (SL), number of kernels per spike (NKS), thousand kernel weight (TKW), and kernels yield per m2 (YM2). The collection was genotyped using a 20,000 (20K) Illumina iSelect SNP array, and 8,662 polymorphic SNP markers were selected for a genome-wide association study (GWAS) to identify QTLs for targeted agronomic traits. Results Out of the total of 237 discovered QTLs, 50 were identified as being stable QTLs for irrigated and rainfed conditions in the Akmola region, Northern Kazakhstan; the identified QTLs were associated with all the studied traits except PH. The results indicate that nine QTLs for HD and 11 QTLs for SMD are presumably novel genetic factors identified in the irrigated and rainfed conditions of Northern Kazakhstan. The identified SNP markers of the QTLs for targeted traits in rainfed conditions can be applied to develop new competitive spring wheat cultivars in arid zones using a marker-assisted selection approach.

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Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates

BMC Plant Biology ◽

10.1186/s12870-019-2135-x ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

A. López-Malvar ◽

A. Butrón ◽

L. F. Samayoa ◽

D. J. Figueroa-Garrido ◽

R. A. Malvar ◽

...

Keyword(s):

Cell Wall ◽

Stem Cell ◽

Genomic Selection ◽

Marker Assisted Selection ◽

Biofuel Production ◽

Genome Wide Association ◽

Genome Wide ◽

Individual Snps ◽

A Genome ◽

Genomic Regions

Abstract Background The structural reinforcement of cell walls by hydroxycinnamates has a significant role in defense against pests and pathogens, but it also interferes with forage digestibility and biofuel production. Elucidation of maize genetic variations that contribute to variation for stem hydroxycinnamate content could simplify breeding for cell wall strengthening by using markers linked to the most favorable genetic variants in marker-assisted selection or genomic selection approaches. Results A genome-wide association study was conducted using a subset of 282 inbred lines from a maize diversity panel to identify single nucleotide polymorphisms (SNPs) associated with stem cell wall hydroxycinnamate content. A total of 5, 8, and 2 SNPs were identified as significantly associated to p-coumarate, ferulate, and total diferulate concentrations, respectively in the maize pith. Attending to particular diferulate isomers, 3, 6, 1 and 2 SNPs were related to 8–O–4 diferulate, 5–5 diferulate, 8–5 diferulate and 8–5 linear diferulate contents, respectively. This study has the advantage of being done with direct biochemical determinations instead of using estimates based on Near-infrared spectroscopy (NIRS) predictions. In addition, novel genomic regions involved in hydroxycinnamate content were found, such as those in bins 1.06 (for FA), 4.01 (for PCA and FA), 5.04 (for FA), 8.05 (for PCA), and 10.03 and 3.06 (for DFAT and some dimers). Conclusions The effect of individual SNPs significantly associated with stem hydroxycinnamate content was low, explaining a low percentage of total phenotypic variability (7 to 10%). Nevertheless, we spotlighted new genomic regions associated with the accumulation of cell-wall-bound hydroxycinnamic acids in the maize stem, and genes involved in cell wall modulation in response to biotic and abiotic stresses have been proposed as candidate genes for those quantitative trait loci (QTL). In addition, we cannot rule out that uncharacterized genes linked to significant SNPs could be implicated in dimer formation and arobinoxylan feruloylation because genes involved in those processes have been poorly characterized. Overall, genomic selection considering markers distributed throughout the whole genome seems to be a more appropriate breeding strategy than marker-assisted selection focused in markers linked to QTL.

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Genome-Wide Association Mapping Identifies Disease-Resistance QTLs in Barley Germplasm from Latin America

Advance in Barley Sciences ◽

10.1007/978-94-007-4682-4_18 ◽

2012 ◽

pp. 209-215 ◽

Cited By ~ 3

Author(s):

Lucía Gutiérrez ◽

Natalia Berberian ◽

Flavio Capettini ◽

Esteban Falcioni ◽

Darío Fros ◽

...

Keyword(s):

Latin America ◽

Disease Resistance ◽

Association Mapping ◽

Genome Wide Association ◽

Resistance Qtls ◽

Genome Wide ◽

Barley Germplasm

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Multi-model genome-wide association and genomic prediction analysis of 16 agronomic, physiological and quality related traits in ICARDA spring wheat

Euphytica ◽

10.1007/s10681-021-02933-6 ◽

2021 ◽

Vol 217 (11) ◽

Author(s):

Admas Alemu ◽

Sufian Suliman ◽

Adel Hagras ◽

Sherif Thabet ◽

Ayed Al-Abdallat ◽

...

Keyword(s):

Heat Stress ◽

Heat Tolerance ◽

Spring Wheat ◽

Genomic Prediction ◽

Marker Assisted Selection ◽

Genome Wide Association ◽

Genome Wide ◽

Chromosome Arm ◽

Yield Quality ◽

Trait Associations

AbstractIdentification and exploration of the genetic architecture of traits related to yield, quality, and drought and heat tolerance is important for yield and quality improvement of wheat through marker-assisted selection. One hundred and ninety-two spring wheat genotypes were tested at two heat-stress locations in Sudan (Wad Medani and Dongula), a drought stress site in Morocco (Marchouch) and a site with high yield potential in Egypt (Sids) in replicated trials during the 2015–2016 and 2016–2017 cropping seasons. A total of 10,577 single nucleotide polymorphism markers identified from the 15 K wheat SNP assay were used in a genome-wide association (GWA) study and genomic prediction for 16 phenotypic traits related to yield, quality and drought and heat tolerance. Significant marker-trait associations were detected across GWAS models for all traits. Most detected marker-trait associations (MTAs) were environment-specific, signifying the presence of high quantitative trait loci-by-environment (QTL x E) interaction. Chromosome arm 5AL had significant multi-model MTAs for grain yield and yield-related traits at the heat-stress locations. Highly significant QTLs were detected on chromosome 2D for waxiness. Homoeologous group 2 and 6 chromosomes were with significant MTAs for grain protein content, gluten content, alveograph strength and Zeleny sedimentation test while chromosome arm 3BL was significant for both Z and W traits. Genomic prediction analysis with ridge regression-best linear unbiased prediction model estimated the breeding values of the studied traits with prediction accuracies ranging from 0.16 for leaf rolling to 0.72 for peduncle length. The identified QTLs could be targeted for marker-assisted selection or further studies aimed at fine mapping and cloning the causative genes and detecting favorable haplotypes with positive effects for agronomic, physiological or quality-related traits.

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Genome-wide association study of leaf rust resistance in Russian spring wheat varieties

BMC Plant Biology ◽

10.1186/s12870-020-02333-3 ◽

2020 ◽

Vol 20 (S1) ◽

Author(s):

Irina N. Leonova ◽

Ekaterina S. Skolotneva ◽

Elena A. Salina

Keyword(s):

Association Study ◽

Leaf Rust ◽

Spring Wheat ◽

Marker Assisted Selection ◽

Rust Resistance ◽

Genome Wide Association Study ◽

Leaf Rust Resistance ◽

Genome Wide Association ◽

Wheat Varieties ◽

Genome Wide

Abstract Background Leaf rust (Puccinia triticina Eriks.) is one of the most dangerous diseases of common wheat worldwide. Three approaches: genome-wide association study (GWAS), marker-assisted selection (MAS) and phytopathological evaluation in field, were used for assessment of the genetic diversity of Russian spring wheat varieties on leaf rust resistance loci and for identification of associated molecular markers. Results The collection, consisting of 100 Russian varieties of spring wheat, was evaluated over three seasons for resistance to the native population of leaf rust specific to the West Siberian region of Russia. The results indicated that most cultivars showed high susceptibility to P. triticina, with severity ratings (SR) of 60S–90S, however some cultivars showed a high level of leaf rust resistance (SR < 20MR-R). Based on the results of genome-wide association studies (GWAS) performed using the wheat 15 K genotyping array, 20 SNPs located on chromosomes 6D, 6A, 6B, 5A, 1B, 2A, 2B and 7A were revealed to be associated with leaf rust resistance. Genotyping with markers developed for known leaf rust resistance genes showed that most of the varieties contain genes Lr1, Lr3a, Lr9, Lr10, Lr17a, Lr20, Lr26 and Lr34, which are not currently effective against the pathogen. In the genome of three wheat varieties, gene Lr6Ai = 2 inherited from Th. intermedium was detected, which provides complete protection against the rust pathogen. It has been suggested that the QTL mapped to the chromosome 5AS of wheat cultivar Tulaikovskaya-zolotistaya, Tulaikovskaya-10, Samsar, and Volgouralskaya may be a new, previously undescribed locus conferring resistance to leaf rust. Obtained results also indicate that chromosome 1BL of the varieties Sonata, Otrada-Sibiri, Tertsiya, Omskaya-23, Tulaikovskaya-1, Obskaya-14, and Sirena may contain an unknown locus that provides a resistance response to local population. Conclusions This study provides new insights into the genetic basis of resistance to leaf rust in Russian spring wheat varieties. The SNPs significantly associated with leaf rust resistance can be used for the development and application of diagnostic markers in marker-assisted selection schemes.

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