A genome-wide association study of hexanal content related to soymilk off-flavours in seed of soybean (Glycine max)

2020 ◽  
Vol 71 (6) ◽  
pp. 552 ◽  
Author(s):  
Zhikun Wang ◽  
Gege Bao ◽  
Chao Yang ◽  
Mingming Yang ◽  
Xue Zhao ◽  
...  
Keyword(s):  
Glycine Max ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Molecular Mechanisms ◽  
Fatty Acid Content ◽  
Soybean Seed ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Hexanal Content

Flavour is an essential quality characteristic of soymilk; however, it contains volatile compounds unacceptable to consumers. Hexanal is the most important flavour compound that gives a sensory beany, grassy flavour in the soymilk. An effective way to reduce hexanal content in soymilk is to screen for and utilise cultivars of soybean (Glycine max (L.) Merr.) with lower hexanal content. The objective of the present study was to dissect the genetic basis of hexanal content in soybean seed by using genome-wide association analysis (GWAS), thereby providing guidance for the selection and breeding of soybean varieties with low hexanal content. We used 24651 single-nucleotide polymorphisms (SNPs) and screened seeds from 111 cultivated soybean accessions to identify quantitative trait nucleotides (QTNs) affecting hexanal content. We discovered 14 novel QTNs located on five different chromosomes that are significantly associated with hexanal content in soybean seed. Among these, 11 QTNs co-localised with quantitative trait loci previously found in linkage or association mapping studies related to protein, oil and/or fatty acid content in soybean seed. We also identified some candidate genes involved in amino acid metabolism, protein content, lipid metabolism and hormone metabolism. Six cultivars with low hexanal content were identified by screening. This is the first GWAS study on hexanal content in soybean seed, and a number of QTNs and candidate genes were identified. Some of these may be useful to breeders for the improvement of marker-assisted breeding efficiency for low hexanal content and may be useful for exploring possible molecular mechanisms underlying hexanal content in soybean seed.

Genetic dissection of 2-heptenal content in soybean (Glycine max) seed through genome-wide association study

2020 ◽  
Vol 71 (10) ◽  
pp. 884
Author(s):  
Zhikun Wang ◽  
Mingming Yang ◽  
Yuanzhuo Wang ◽  
Chao Yang ◽  
Xue Zhao ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Study ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Fatty Acid Content ◽  
Soybean Seed ◽  
Genome Wide Association ◽  
Quality Characteristic ◽  
Genome Wide ◽  
A Genome

Association analysis is an alternative to conventional, family-based methods for detecting the location of gene(s) or quantitative trait loci (QTLs), and provides relatively high resolution in terms of defining the genome position of a gene or QTL. Flavour is an essential quality characteristic of soymilk; however, soymilk contains volatile compounds unacceptable to consumers. One of main constituents in the volatiles of normal soymilk is 2-heptenal, which is thought to be a degradative oxidation product of polyunsaturated acids. In this study, a genome-wide association study using 24651 single-nucleotide polymorphisms (SNPs) was performed to identify quantitative trait nucleotides (QTNs) controlling 2-heptenal content in soybean (Glycine max (L.) Merr.) seed from a natural population of 110 soybean germplasm accessions. We detected 62 significant QTNs located on 18 different chromosomes that are significantly associated with 2-heptenal content in soybean seed. Among these, 17 QTNs co-localised with QTLs previously found to be related to protein, oil and/or fatty acid content in soybean seed. We also identified some candidate genes involved in lipid metabolism. These findings further our understanding of the genetic basis of 2-heptenal content in soybean seed and the improvement of marker-assisted breeding efficiency, which will be important for breeding soybean cultivars with low 2-heptenal content.

scholarly journals A Genome-Wide Association Study Identifies Quantitative Trait Loci Affecting Hematological Traits in Camelus bactrianus

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 96 ◽  
Author(s):  
Fucheng Guo ◽  
Liang Ming ◽  
Rendalai Si ◽  
Li Yi ◽  
Jing He ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Gobi Desert ◽  
Camelus Bactrianus ◽  
Genome Wide ◽  
A Genome ◽  
Bactrian Camels

Bactrian camels (Camelus bactrianus) are one of the few large livestock species that can survive in the Gobi Desert. Animal immunity and disease resistance are related to hematological traits, which are also associated with tolerance observed in Bactrian camels. However, no genome-wide association studies have examined the genetic mechanism of the immune capability of Bactrian camels. In the present study, we used genotyping-by-sequencing data generated from 366 Bactrian camel accessions to perform a genome-wide association study for 17 hematological traits. Of the 256,616 single-nucleotide polymorphisms (SNPs) obtained, 1,635 trait–SNP associations were among the top quantitative trait locus candidates. Lastly, 664 candidate genes associated with 13 blood traits were identified. The most significant were ZNF772, MTX2, ESRRG, MEI4, IL11, FRMPD4, GABPA, NTF4, CRYBG3, ENPP5, COL16A1, and CD207. The results of our genome-wide association study provide a list of significant SNPs and candidate genes, which offer valuable information for further dissection of the molecular mechanisms that regulate the camel’s hematological traits to ultimately reveal their tolerance mechanisms.

Genome-wide association mapping and candidate gene analysis for seed shape in soybean (Glycine max)

2019 ◽  
Vol 70 (8) ◽  
pp. 684 ◽  
Author(s):  
Xue Zhao ◽  
Wenjing Li ◽  
Xiaoyue Zhao ◽  
Jinyang Wang ◽  
Zhiyang Liu ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Analysis ◽  
Quantitative Trait ◽  
Molecular Mechanisms ◽  
Environmental Stability ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Seed Shape ◽  
Genome Wide ◽  
Genomic Regions

Seed shape (SS) of soybean (Glycine max (L.) Merr.) is an important morphological trait that significantly affects the quality of marketable seed. Study of the genetic architecture of SS is important and basic to soybean molecular breeding. In the present study, a natural soybean population of 202 diverse accessions mainly from China was used to analyse the genetic basis of SS via genome-wide association analysis (GWAS), which was based on single-nucleotide polymorphisms (SNP) generated by specific-locus amplified fragment sequencing method. In total, 27335 SNPs were finally identified with minor allele frequencies >5%. By using GWAS, 14 quantitative trait nucleotides (QTNs) were identified to be associated with seed length, 13 with seed width and 21 with seed thickness in four tested environments. Among these QTNs, 21 QTNs overlapped or were located in the linked genomic regions of the reported quantitative trait loci related to SS or seed weight; and the other 27 QTNs were novel loci for SS. Ten QTNs showed environmental stability and were detected under at least two environments. In total, 83 genes were predicted in the 200-kbp flanking region of six stable QTNs that could be detected under >three environments. Gene-based association analysis was performed by using 38 accessions of diverse SS; 778 SNPs were found in the 83 genes based on 38 accessions, and 270 SNPs from 41 genes were found significantly associated with SS. Twenty-eight genes were environmentally stable and/or pleiotropic in controlling two or more SS-related traits at the same time. The identified loci along with the candidate genes could be of great value for studying the molecular mechanisms underlying SS and improving the potential seed yield of soybean.

scholarly journals Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill]

2019 ◽  
Author(s):  
Xue Zhao ◽  
Hairan Dong ◽  
Hong Chang ◽  
Jingyun Zhao ◽  
Weili Teng ◽  
...  
Keyword(s):  
Glycine Max ◽  
Candidate Genes ◽  
Seed Weight ◽  
Growth Regulation ◽  
Genome Wide Association ◽  
Starch Accumulation ◽  
Genome Wide ◽  
A Genome ◽  
Glycine Max L ◽  
Soybean Food

Abstract Background: The hundred seed weight (HSW) is one of the yield components of soybean [Glycine max (L.) Merrill] and is especially critical for various soybean food types. In this study, a representative sample consisting of 185 accessions was selected from Northeast China and analysed in three tested environments to determine the quantitative trait nucleotide (QTN) of HSW through a genome-wide association study (GWAS). Result: A total of 24,180 single nucleotide polymorphisms (SNPs) with minor allele frequencies greater than 0.2 and missing data less than 3% were utilized to estimate linkage disequilibrium (LD) levels in the tested association panel. Thirty-four association signals were identified as associated with HSW via GWAS. Among them, nineteen QTNs were novel, and another fifteen QTNs were overlapped or located near the genomic regions of known HSW QTL. A total of 237 genes, derived from 31 QTNs and located near peak SNPs from the three tested environments in 2015 and 2016, were considered candidate genes, were related to plant growth regulation, hormone metabolism, cell, RNA, protein metabolism, development, starch accumulation, secondary metabolism, signalling, and the TCA cycle, some of which have been found to participate in the regulation of HSW. A total of 106 SNPs from 16 candidate genes were significantly associated with HSW in soybean. Conclusions: The identified loci with beneficial alleles and candidate genes might be valuable for the molecular network and MAS of HSW.

scholarly journals Genome-Wide Association Study for Ultraviolet-B Resistance in Soybean (Glycine max L.)

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1335
Author(s):  
Taeklim Lee ◽  
Kyung Do Kim ◽  
Ji-Min Kim ◽  
Ilseob Shin ◽  
Jinho Heo ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Leaf Shape ◽  
Ultraviolet B ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Glycine Max L

The depletion of the stratospheric ozone layer is a major environmental issue and has increased the dosage of ultraviolet-B (UV-B) radiation reaching the Earth’s surface. Organisms are negatively affected by enhanced UV-B radiation, and especially in crop plants this may lead to severe yield losses. Soybean (Glycine max L.), a major legume crop, is sensitive to UV-B radiation, and therefore, it is required to breed the UV-B-resistant soybean cultivar. In this study, 688 soybean germplasms were phenotyped for two categories, Damage of Leaf Chlorosis (DLC) and Damage of Leaf Shape (DLS), after supplementary UV-B irradiation for 14 days. About 5% of the germplasms showed strong UV-B resistance, and GCS731 was the most resistant genotype. Their phenotypic distributions showed similar patterns to the normal, suggesting UV-B resistance as a quantitative trait governed by polygenes. A total of 688 soybean germplasms were genotyped using the Axiom® Soya 180K SNP array, and a genome-wide association study (GWAS) was conducted to identify SNPs significantly associated with the two traits, DLC and DLS. Five peaks on chromosomes 2, 6, 10, and 11 were significantly associated with either DLC or DLS, and the five adjacent genes were selected as candidate genes responsible for UV-B resistance. Among those candidate genes, Glyma.02g017500 and Glyma.06g103200 encode cryptochrome (CRY) and cryptochrome 1 (CRY1), respectively, and are known to play a role in DNA repair during photoreactivation. Real-time quantitative RT-PCR (qRT-PCR) results revealed that CRY1 was expressed significantly higher in the UV-B-resistant soybean compared to the susceptible soybean after 6 h of UV-B irradiation. This study is the first GWAS report on UV-B resistance in soybean, and the results will provide valuable information for breeding UV-B-resistant soybeans in preparation for climate change.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

scholarly journals Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 318
Author(s):  
Tae-Ho Ham ◽  
Yebin Kwon ◽  
Yoonjung Lee ◽  
Jisu Choi ◽  
Joohyun Lee
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Matrix Analysis ◽  
Rice Seedlings ◽  
Genome Wide ◽  
A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

scholarly journals Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Peng Xu ◽  
Qi Guo ◽  
Shan Meng ◽  
Xianggui Zhang ◽  
Zhenzhen Xu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Genetic Variations ◽  
Genome Wide Association ◽  
Cotton Production ◽  
Fresh Matter ◽  
Salt Stress Response ◽  
Genome Wide ◽  
A Genome

Abstract Background Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance. Results In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on 2 years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (−log10p > 4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response. Conclusions These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.

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