GWAS of pod morphological and color characters in common bean

Abstract Background Common bean (Phaseolus vulgaris L.) is an important legume species which can be consumed as immature pods and dry seeds after re-hydration and cooking. Many genes and QTL, and epistatic interactions among them, condition pod morphological traits. However, not all them have been mapped or validated nor candidate genes proposed. We sought to investigate the genomic regions conditioning pod morphological and color characters through GWAS. Results Single and multi-locus genome wide association analysis was used to investigate pod traits for a set of 301 bean lines of the Spanish Diversity Panel (SDP). The SDP was genotyped with 32,812 SNPs obtained from Genotyping by Sequencing. The panel was grown in two seasons and phenotypic data were recorded for 17 fresh pods traits grouped in four pod characters: pod length, pod cross-section, pod color, and number of seeds per pod. In all, 23 QTL for pod length, 6 for cross-section, 18 for pod color, 6 for number of seeds per pod and 9 associated to two or more pod characters were detected. Most QTL were located in the telomeric region of chromosomes Pv01, Pv02, Pv04, Pv08, Pv09 and Pv10. Eighteen detected QTL co-localized with 28 previously reported QTL. Twenty-one potential candidate genes involving developmental processes were detected underlying 11 QTL for pod morphological characters, four of them homologous to A. thaliana genes FIS2, SPL10, TTG2 and AML4 affecting silique size. Eight potential candidate genes involved in pigment synthesis, were found underlying five QTL for pod color. Conclusions GWAS for pod morphological and color characters in the bean Spanish Diversity Panel revealed 62 QTL, 18 co-localized with previously reported QTL, and 16 QTL were underlain by 25 candidate genes. Overall 44 new QTL identified and 18 existing QTL contribute to a better understanding of the complex inheritance of pod size and color traits in common bean and open the opportunity for future validation works.

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GWAS Of Pod Morphological and Color Characters in Common Bean

10.21203/rs.3.rs-182844/v1 ◽

2021 ◽

Author(s):

Carmen García-Fernández ◽

Ana Campa ◽

Alvaro Soler Garzón ◽

Phil Miklas ◽

Juan Jose Ferreira

Keyword(s):

Common Bean ◽

Candidate Genes ◽

Cross Section ◽

Genotyping By Sequencing ◽

Telomeric Region ◽

Phenotypic Data ◽

Pigment Synthesis ◽

Diversity Panel ◽

Pod Length ◽

Number Of Seeds

Abstract BackgroundCommon bean (Phaseolus vulgaris L.) is an important legume species which can be consumed as immature pods and dry seeds after re-hydration and cooking. Many genes and QTL, and epistatic interactions among them, condition pod morphological traits. However, not all them have been mapped or validated nor candidate genes proposed. We sought to investigate the genomic regions conditioning pod morphological and color characters through GWAS.ResultsSingle and multi-locus genome wide association analysis was used to investigate pod traits for a set of 301 bean lines of the Spanish Diversity Panel (SDP). The SDP was genotyped with 32,812 SNPs obtained from Genotyping by Sequencing. The panel was grown in two seasons and phenotypic data were recorded for 17 fresh pods traits grouped in four pod characters: pod length, pod cross-section, pod color, and number of seeds per pod. In all, 23 QTL for pod length, 6 for cross-section, 18 for pod color, 6 for number of seeds per pod and 9 associated to two or more pod characters were detected. Most QTL were located in the telomeric region of chromosomes Pv01, Pv02, Pv04, Pv08, Pv09 and Pv10. Eighteen detected QTL co-localized with previously reported QTL. Twenty-one candidate genes involving developmental processes were detected underlying 11 QTL for pod morphological characters, four of them homologous to A. thaliana genes FIS2, SPL10, TTG2 and AML4 affecting silique size. Eight candidate genes involved in pigment synthesis, were found underlying five QTL for pod color.ConclusionsGWAS for pod morphological and color characters in the bean Spanish Diversity Panel revealed 62 QTL, 18 co-localized with previously reported QTL, and 16 QTL were underlain by 25 candidate genes. Overall new QTL identified and existing QTL validated contribute to a better understanding of the complex inheritance of pod size and color traits in common bean.

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Linked candidate genes of different functions for white mold resistance in common bean (Phaseolus vulgaris. L) are identified by QTL-based pooled sequencing

10.21203/rs.2.13657/v1 ◽

2019 ◽

Author(s):

Atena Oladzadabbasabadi ◽

Sujan Mamidi ◽

Phillip N. Miklas ◽

Rian Lee ◽

Phillip McClean

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Candidate Genes ◽

White Mold ◽

Potential Candidate ◽

Sequencing Analysis ◽

Phaseolus Vulgaris L ◽

Pooled Sequencing ◽

Physiological Resistance ◽

Mold Resistance

Abstract Background White mold (WM) is a major disease in common bean ( Phaseolus vulgaris L.), and its complex quantitative genetic control has limited the development of WM resistant cultivars. WM2.2 is one of the nine meta-QTL that has a major effect on WM tolerance. This QTL explains up to 35% of the phenotypic variation and was previously mapped to a large interval on Pv02. Our objective was to narrow the interval of this QTL using QTL-based bulk segregant analysis.Results The phenotypic and genotypic data from two RIL populations (R31 and Z0726-9), which possess different genetic backgrounds for white mold resistance, were used to select resistant and susceptible lines to generate subpopulations for bulk DNA sequencing, and reads were aligned against the sequence of the resistance parent. The QTL physical intervals for each RIL population were mapped by fixed SNPs in 10kb-2kb sliding windows. WM2.2 QTL was split into two regions WM2.2a (3.54-4.56 Mbp; euchromatic) and WM 2.2b (12.19 to 26.41 Mbp; heterochromatic) in populations R31 and Z0726-9, respectively. For each QTL interval, the possible functional contribution of significant non-synonymous and synonymous polymorphisms was investigated. Gene models encoding for pentatricopeptide repeat, gibberellin 2-oxidase, and heat-shock proteins are the likely candidate genes associated with WM2.2a resistance. A TIR-NBS-LRR class of disease resistance protein and a EF-TU receptor are potential candidate genes associated with WM2.2b resistance and most likely trigger a physiological resistance response to WM.Conclusion QTL-based pooled sequencing analysis revealed that the large genomic region associated with WM2.2 meta QTL consists of two major QTL each associated with a different WM resistance function. WM2.2a region is most likely associated with avoidance mechanisms while WM2.2b region triggers physiological resistance.

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Genetic Dissection of Drought Resistance of Common Bean at the Seedling Stage by Genome-wide Association Study

10.21203/rs.3.rs-752443/v1 ◽

2021 ◽

Author(s):

Lei Wu ◽

Yujie Chang ◽

Lanfen Wang ◽

Shumin Wang ◽

Jing Wu

Keyword(s):

Common Bean ◽

Candidate Genes ◽

Drought Resistance ◽

Survival Rates ◽

Seedling Stage ◽

Genome Wide Association ◽

Potential Candidate ◽

Chromosome 11 ◽

Genome Wide ◽

A Genome

Abstract A variety of adverse conditions, including drought stress, severely affect common bean production. Molecular breeding for drought resistance has been proposed as an effective and practical way to improve the drought resistance of common bean. A genome-wide association analysis was conducted to identify drought-related loci based on survival rates at the seedling stage using a natural population consisting of 400 common bean accessions and 3832340 SNPs. The coefficient of variation ranged from 40.90% to 56.22% for survival rates in three independent experiments. A total of 12 associated loci containing 89 significant SNPs were identified for survival rates at the seedling stage. Four loci overlapped in the region of the QTLs reported to be associated with drought resistance. According to the expression profiles, gene annotations and references of the functions of homologous genes in Arabidopsis, 39 genes were considered potential candidate genes selected from 199 genes annotated within all associated loci. A stable locus (Locus_10) was identified on chromosome 11, which contained LEA, aquaporin, and proline-rich protein genes. We further confirmed the drought-related function of an aquaporin (PvXIP1;2) located at Locus_10 by expression pattern analysis, phenotypic analysis of PvXIP1;2-overexpressing Arabidopsis and Agrobacterium rhizogenes-mediated hairy root transformation systems, indicating that the association results can facilitate the efficient identification of genes related to drought resistance. These loci and their candidate genes provide a foundation for crop improvement via breeding for drought resistance in common bean.

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Morphological variability and phylogenetic analysis in Common bean (Phaseolus vulgaris L.)

Legume Research - An International Journal ◽

10.18805/lr-3421 ◽

2018 ◽

Cited By ~ 1

Author(s):

S. M. Razvi ◽

M. N. Khan ◽

M. Ashraf Bhat ◽

Mushtaq Ahmad ◽

S.A. N. Ganaie ◽

...

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Protein Content ◽

Seed Yield ◽

Seed Weight ◽

Morphological Variability ◽

Days To Maturity ◽

Pod Length ◽

100 Seed Weight ◽

Number Of Seeds

Thirteen common bean (Phaseolus vulgaris) accessions collected from different ecological regions of Jammu and Kashmir were evaluated at four diverse locations during kharief 2009. Significant variation was observed for most of the morphological traits. Estimates of heritability (bs) were high (>60 %) for all the traits except pod length. The expected genetic gain (per cent of mean) was high (>30 %) for days to maturity, number of pods plant-1, number of seeds pod-1, 100-seed weight and seed yield plant-1 while it was moderate (10.0-30.0%) for days to 50 per cent flowering, number of branches plant-1, pod length and protein content. Seed yield plant-1 was observed to have a highly positive and significant correlation both at phenotypic and genotypic levels with number of pods plant-1, pod length, number of seeds pod-1 and 100-seed weight. But negative and significant correlations with days to 50 per cent flowering and days to maturity were estimated from pooled analysis. Classification of accessions led to the formation of two clusters wherein the maximum number 7 accessions were grouped in cluster I and the remaining six were grouped in cluster II. Analysis of traits contributing maximum to the divergence revealed that traits viz., 100-seed weight (37.10%), protein content (15.26%), number of seeds pod-1 (11.28%) and days to maturity (10.14%) to contribute to the divergence in the present experimental material.

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Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw

Biotechnology for Biofuels ◽

10.1186/s13068-020-01807-8 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Duong T. Nguyen ◽

Leonardo D. Gomez ◽

Andrea Harper ◽

Claire Halpin ◽

Robbie Waugh ◽

...

Keyword(s):

Candidate Genes ◽

Lignocellulosic Biomass ◽

Rice Straw ◽

Lignin Content ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Potential Candidate ◽

Rice Breeding ◽

Diversity Panel ◽

Genome Wide

Abstract Background The conversion of lignocellulosic biomass from agricultural waste into biofuels and chemicals is considered a promising way to provide sustainable low carbon products without compromising food security. However, the use of lignocellulosic biomass for biofuel and chemical production is limited by the cost-effectiveness of the production process due to its recalcitrance to enzymatic hydrolysis and fermentable sugar release (i.e., saccharification). Rice straw is a particularly attractive feedstock because millions of tons are currently burned in the field each year for disposal. The aim of this study was to explore the underlying natural genetic variation that impacts the recalcitrance of rice (Oryza sativa) straw to enzymatic saccharification. Ultimately, we wanted to investigate whether we could identify genetic markers that could be used in rice breeding to improve commercial cultivars for this trait. Here, we describe the development and characterization of a Vietnamese rice genome-wide association panel, high-throughput analysis of rice straw saccharification and lignin content, and the results from preliminary genome-wide association studies (GWAS) of the combined data sets. We identify both QTL and plausible candidate genes that may have an impact on the saccharification of rice straw. Results We assembled a diversity panel comprising 151 rice genotypes (Indica and Japonica types) from commercial, historical elite cultivars, and traditional landraces grown in Vietnam. The diversity panel was genotyped using genotype by sequencing (GBS) methods yielding a total of 328,915 single nucleotide polymorphisms (SNPs). We collected phenotypic data from stems of these 151 genotypes for biomass saccharification and lignin content. Using GWAS on the indica genotypes over 2 years we identified ten significant QTL for saccharification (digestibility) and seven significant QTL for lignin. One QTL on chromosome 11 occurred in both GWAS for digestibility and for lignin. Seven QTL for digestibility, on CH2, CH6, CH7, CH8, and CH11, were observed in both years of the study. The QTL regions for saccharification include three potential candidate genes that have been previously reported to influence digestibility: OsAT10; OsIRX9; and OsMYB58/63-L. Conclusions Despite the difficulties associated with multi-phasic analysis of complex traits in novel germplasm, a moderate resolution GWAS successfully identified genetic associations encompassing both known and/or novel genes involved in determining the saccharification potential and lignin content of rice straw. Plausible candidates within QTL regions, in particular those with roles in cell wall biosynthesis, were identified but will require validation to confirm their value for application in rice breeding.

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STUDY OF EFFECT OF EMS, MMS AND GR ON YIELD CONTRIBUTING TRAITS IN URDBEAN, VIGNA MUNGO

FLORA AND FAUNA ◽

10.33451/florafauna.v23i1pp115-118 ◽

2017 ◽

Vol 23 (1) ◽

Author(s):

A. B. SAGADE

Keyword(s):

Plant Height ◽

Seed Yield ◽

Seed Weight ◽

Inhibitory Effect ◽

Individual Plant ◽

Mean Values ◽

Methane Sulphonate ◽

Pod Length ◽

100 Seed Weight ◽

Number Of Seeds

The study of the effect of three well known mutagens, ethyl methane sulphonate (EMS), methyl methane sulphonate (MMS) and gamma rays (GR) on the yield contributing traits of the urdbean variety TPU-4 were carried out in the M3 generation. Effect of selected mutagenic treatments/doses of EMS (0.02, 0.03 and 0.04 M), MMS (0.0025, 0.05 and 0.01 M) and (GR) (30, 40 and 50 KR) on different yield contributing traits like plant height, plant spread, number of pods per plant, pod length, number of seeds per pod, seed yield per plant and 100 seed weight were analyzed in the M3 populations of the variety TPU-4. Seeds of M2 plants and control were harvested separately and sown to raise M3 population.. Genetic variabilty in the mutagen administered M3 progeny of the urdbean variety TPU-4 was analyzed by employing statistical methods. Data on mean values and shift in the mean of seven quantitative traits was evaluated on individual plant basis. The experimental findings revealed that concentrations / dose of the all these mutagens showed inhibitory effect on plant height, number of pods per plant, pod length and number of seeds per pod. Lower concentrations of mutagens exerted a promotory effect on plant spread, 100 seed weight and seed yield per plant while higher concentrations of these mutagens inhibited them to different extent.

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Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

Scientific Reports ◽

10.1038/s41598-021-85921-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Raju Bheemanahalli ◽

Montana Knight ◽

Cherryl Quinones ◽

Colleen J. Doherty ◽

S. V. Krishna Jagadish

Keyword(s):

Grain Size ◽

Candidate Genes ◽

Gene Network ◽

Genome Wide Association ◽

Potential Candidate ◽

Genetic Loci ◽

Stay Green ◽

Yield And Quality ◽

Genome Wide ◽

Wide Range

AbstractHigh night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.

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Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

Scientific Reports ◽

10.1038/s41598-021-91373-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lili Du ◽

Tianpeng Chang ◽

Bingxing An ◽

Mang Liang ◽

Xinghai Duan ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Molecular Mechanism ◽

Meat Quality ◽

Relevant Literature ◽

Transcriptome Profiling ◽

Water Holding Capacity ◽

Potential Candidate ◽

Protein Protein Interaction ◽

Water Holding

AbstractWater holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

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