Comprehensive Identification of Drought Tolerance QTL-Allele and Candidate Gene Systems in Chinese Cultivated Soybean Population

Drought is one of the most important factors affecting plant growth and productivity. The previous results on drought tolerance (DT) genetic system in soybean indicated a complex of genes not only few ones were involved in the trait. This study is featured with a relatively thorough identification of QTL-allele/candidate-gene system using an efficient restricted two-stage multi-locus multi-allele genome-wide association study, on two comprehensive DT indicators, membership index values of relative plant weight (MPW) and height (MPH), instead of a single biological characteristic, in a large sample (564 accessions) of the Chinese cultivated soybean population (CCSP). Based on 24,694 multi-allele markers, 75 and 64 QTL with 261 and 207 alleles (2–12/locus) were detected for MPW and MPH, explaining 54.7% and 47.1% of phenotypic variance, respectively. The detected QTL-alleles were organized into a QTL-allele matrix for each indicator, indicating DT is a super-trait conferred by two (even more) QTL-allele systems of sub-traits. Each CCSP matrix was separated into landrace (LR) and released cultivar (RC) sub-matrices, which showed significant differentiation in QTL-allele constitutions, with 58 LR alleles excluded and 16 new ones emerged in RC. Using the matrices, optimal crosses with great DT transgressive recombinants were predicted. From the detected QTL, 177 candidate genes were annotated and validated with quantitative Real-time PCR, and grouped into nine categories, with ABA and stress responders as the major parts. The key point of the above results is the establishment of relatively full QTL-allele matrices composed of numerous gene functions jointly conferring DT, therefore, demonstrates the complexity of DT genetic system and potential of CCSP in DT breeding.

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Genome-Wide Association Analysis Identified BMPR1A as a Novel Candidate Gene Affecting the Number of Thoracic Vertebrae in a Large White × Minzhu Intercross Pig Population

Animals ◽

10.3390/ani10112186 ◽

2020 ◽

Vol 10 (11) ◽

pp. 2186

Author(s):

Qian Liu ◽

Jingwei Yue ◽

Naiqi Niu ◽

Xin Liu ◽

Hua Yan ◽

...

Keyword(s):

Candidate Gene ◽

Genome Wide Association Study ◽

Splice Variants ◽

Genome Wide Association ◽

Thoracic Vertebrae ◽

Phenotypic Variance ◽

Nucleotide Polymorphisms ◽

Large White ◽

Genome Wide ◽

A Genome

The number of vertebrae (NV), especially the number of thoracic vertebrae (NTV), varies among pig breeds. The NTV is controlled by vertebral segmentation and the number of somites during embryonic development. Although there is a high correlation between the NTV and NV, studies on a fixed NV have mainly considered the absolute numbers of thoracic vertebrae instead of vertebral segmentation. Therefore, this study aimed to discover variants associated with the NTV by considering the effect of the NV in pigs. The NTV and NV of 542 F2 individuals from a Large White × Minzhu pig crossbreed were recorded. All animals were genotyped for VRTN g.19034 A > C, LTBP2 c.4481A > C, and 37 missense or splice variants previously reported in a 951-kb interval on SSC7 and 147 single nucleotide polymorphisms (SNPs) on SSC14. To identify NTV-associated SNPs, we firstly performed a genome-wide association study (GWAS) using the Q + K (population structure + kinship matrix) model in TASSEL. With the NV as a covariate, the obtained data were used to identify the SNPs with the most significant genome-wide association with the NTV by performing a GWAS on a PorcineSNP60K Genotyping BeadChip. Finally, a conditional GWAS was performed by fixing this SNP. The GWAS showed that 31 SNPs on SSC7 have significant genome-wide associations with the NTV. No missense or splice variants were found to be associated with the NTV significantly. A linkage disequilibrium analysis suggested the existence of quantitative trait loci (QTL) in a 479-Kb region on SSC7, which contained a critical candidate gene FOS for the NTV in pigs. Subsequently, a conditional GWAS was performed by fixing M1GA0010658, the most significant of these SNPs. Two SNPs in BMPR1A were found to have significant genome-wide associations and a significant dominant effect. The leading SNP, S14_87859370, accounted for 3.86% of the phenotypic variance. Our study uncovered that regulation variants in FOS on SSC7 and in BMPR1A on SSC14 might play important roles in controlling the NTV, and thus these genetic factors may be harnessed for increasing the NTV in pigs.

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QTL Mapping and Candidate Gene Analysis for Alkali Tolerance in Japonica Rice at the bud Stage Based on Linkage Mapping and Genome-Wide Association Study

Rice ◽

10.1186/s12284-020-00412-5 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Xianwei Li ◽

Hongliang Zheng ◽

Wenshen Wu ◽

Hualong Liu ◽

Jingguo Wang ◽

...

Keyword(s):

Qtl Mapping ◽

Association Study ◽

Candidate Gene ◽

Linkage Mapping ◽

Genome Wide Association Study ◽

Gene Analysis ◽

Genome Wide Association ◽

Japonica Rice ◽

Genome Wide ◽

Alkali Tolerance

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Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage

Rice ◽

10.1186/s12284-020-00433-0 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Leila Nayyeripasand ◽

Ghasem Ali Garoosi ◽

Asadollah Ahmadikhah

Keyword(s):

Association Study ◽

Candidate Gene ◽

Candidate Genes ◽

Salinity Tolerance ◽

Genome Wide Association Study ◽

Dry Weight ◽

Genome Wide Association ◽

Vegetative Stage ◽

Genome Wide ◽

Genomic Regions

Abstract Background Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q + K) model. Results Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79–42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K+ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified. Conclusion Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.

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Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

10.21203/rs.2.24272/v1 ◽

2020 ◽

Author(s):

Aditi Bhandari ◽

Nitika Sandhu ◽

Jérôme Bartholome ◽

Tuong-Vi Cao-Hamadoun ◽

Nourollah Ahmadi ◽

...

Keyword(s):

Grain Yield ◽

Field Experiments ◽

Genome Wide Association Study ◽

Reproductive Stage ◽

Phenotypic Variance ◽

Rice Varieties ◽

Drought Tolerant ◽

Genome Wide ◽

Close Proximity ◽

Genomic Regions

Abstract Background Reproductive-stage drought stress is a major impediment to rice production globally. Conventional and marker-assisted breeding strategies for developing drought tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles and understanding their interactions with genetic backgrounds for contributing to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage drought. A diverse set of 280 indica-aus accessions was phenotyped for grain yield and nine yield-related traits under normal condition and under two managed drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. Results The study identified a total of 220 significant MTAs and candidate gene analysis within 200kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 47 genes, 4 earlier reported major grain yield QTLs and 8 novel QTLs for 10 traits. The significant MTAs were majorly located on chromosomes 1, 2, 5, 6, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related traits, except flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding program targeting grain yield improvement under drought. Conclusion These results provide a promising insight into the complex-genetic architecture of grain yield under reproductive-stage drought under different environments. Validation of major genomic regions reported in the study can be effectively used to develop drought tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

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Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage

Rice ◽

10.1186/s12284-021-00538-0 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Dan Wang ◽

Zhuo Liu ◽

Yinghui Xiao ◽

Xionglun Liu ◽

Yue Chen ◽

...

Keyword(s):

Candidate Gene ◽

Cold Tolerance ◽

Genome Wide Association Study ◽

Gene Knockout ◽

Micro Rna ◽

Negative Regulator ◽

Bud Burst ◽

Rab Protein ◽

Genome Wide ◽

Direct Seeded

AbstractCold tolerance at the bud burst stage (CTB) is a key trait for direct-seeded rice. Although quantitative trait loci (QTL) affecting CTB in rice have been mapped using traditional linkage mapping and genome-wide association study (GWAS) methods, the underlying genes remain unknown. In this study, we evaluated the CTB phenotype of 339 cultivars in the Rice Diversity Panel II (RDP II) collection. GWAS identified four QTLs associated with CTB (qCTBs), distributed on chromosomes 1–3. Among them, qCTB-1-1 overlaps with Osa-miR319b, a known cold tolerance micro RNA gene. The other three qCTBs have not been reported. In addition, we characterised the candidate gene OsRab11C1 for qCTB-1-2 that encodes a Rab protein belonging to the small GTP-binding protein family. Overexpression of OsRab11C1 significantly reduced CTB, while gene knockout elevated CTB as well as cold tolerance at the seedling stage, suggesting that OsRab11C1 negatively regulates rice cold tolerance. Molecular analysis revealed that OsRab11C1 modulates cold tolerance by suppressing the abscisic acid signalling pathway and proline biosynthesis. Using RDP II and GWAS, we identified four qCTBs that are involved in CTB and determined the function of the candidate gene OsRab11C1 in cold tolerance. Our results demonstrate that OsRab11C1 is a negative regulator of cold tolerance and knocking out of the gene by genome-editing may provide enhanced cold tolerance in rice.

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Genetics of Germination and Seedling Traits under Drought Stress in a MAGIC Population of Maize

Plants ◽

10.3390/plants10091786 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1786

Author(s):

Soumeya Rida ◽

Oula Maafi ◽

Ana López-Malvar ◽

Pedro Revilla ◽

Meriem Riache ◽

...

Keyword(s):

Drought Tolerance ◽

Genome Wide Association Study ◽

Genetic Regulation ◽

Breeding Programs ◽

Seedling Traits ◽

Genome Wide ◽

A Genome ◽

Positive Correlations ◽

Genomic Regions ◽

Magic Population

Drought is one of the most detrimental abiotic stresses hampering seed germination, development, and productivity. Maize is more sensitive to drought than other cereals, especially at seedling stage. Our objective was to study genetic regulation of drought tolerance at germination and during seedling growth in maize. We evaluated 420 RIL with their parents from a multi-parent advanced generation inter-cross (MAGIC) population with PEG-induced drought at germination and seedling establishment. A genome-wide association study (GWAS) was carried out to identify genomic regions associated with drought tolerance. GWAS identified 28 and 16 SNPs significantly associated with germination and seedling traits under stress and well-watered conditions, respectively. Among the SNPs detected, two SNPs had significant associations with several traits with high positive correlations, suggesting a pleiotropic genetic control. Other SNPs were located in regions that harbored major QTLs in previous studies, and co-located with QTLs for cold tolerance previously published for this MAGIC population. The genomic regions comprised several candidate genes related to stresses and plant development. These included numerous drought-responsive genes and transcription factors implicated in germination, seedling traits, and drought tolerance. The current analyses provide information and tools for subsequent studies and breeding programs for improving drought tolerance.

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