Genome-wide association study of physical and microstructure-related traits in peanut shell

2021 ◽  
pp. 1-11
Author(s):  
Kailu Cui ◽  
Feiyan Qi ◽  
Ziqi Sun ◽  
Jingjing Feng ◽  
Bingyan Huang ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Potential Contribution ◽  
Peanut Shell ◽  
Nucleotide Polymorphisms ◽  
B Genome ◽  
Genome Wide

Abstract Peanut shell plays key roles in protecting the seed from diseases and pest infestation but also in the processing of peanut and is an important byproduct of peanut production. Most studies on peanut shell have focused on the utilization of its chemical applications, but the genetic basis of shell-related traits is largely unknown. A panel of 320 peanut (Arachis hypogaea) accessions including var. hypogaea, var. vulgaris, var. fastigiata and var. hirsuta was used to study the genetic basis of two physical and five microstructure-related traits in peanut shell. Significant phenotypic differences were revealed among the accessions of var. hypogaea, var. hirsuta, var. vulgaris and var. fastigiata for mechanical strength, thickness, three sclerenchymatous layer projections and main cell shape of the sclerenchymatous layer. We identified 10 significant single nucleotide polymorphisms (SNPs) through genome-wide association study (P < 5.0 × 10−6) combining the shell-related traits and high-quality SNPs. In total, 192 genes were located in physical proximity to the significantly associated SNPs, and 11 candidate genes were predicted related to their potential contribution to the development and structure of the peanut shell. All SNPs were detected on the B genome demonstrating the biased contribution of the B genome for the phenotypical make-up of peanut. Exploring the newly identified candidate genes will provide insight into the molecular pathways that regulate peanut shell-related traits and provide valuable information for molecular marker-assisted breeding of an improved peanut shell.

scholarly journals Genome-wide Association Study and Possible Candidate Genes for Root Color and Carotenoid Contents in Japanese Orange Carrot F2 Populations

2021 ◽  
Author(s):  
Taeko Shibaya ◽  
Chika Kuroda ◽  
Hisano Tsuruoka ◽  
Chiharu Minami ◽  
Akiko Obara ◽  
...  
Keyword(s):  
Amino Acid ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Carotenoid Biosynthesis ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Visual Evaluation ◽  
Genome Wide ◽  
A Genome

Abstract Carrot is a major source of provitamin A in a human diet. Two of the most important traits for carrot breeding are carotenoid contents and root color. To examine genomic regions related to these traits and develop DNA markers for carrot breeding, we performed a genome-wide association study (GWAS) using genome-wide single-nucleotide polymorphisms (SNPs) in two F2 populations, both derived from crosses of orange root carrots bred by a Japanese seed company. The GWAS revealed 21 significant associations, and the physical position of some associations suggested two possible candidate genes. An Orange (Or) gene was a possible candidate for visual color evaluation and the α- and β-carotene contents. Sanger sequencing detected a new allele of Or with an SNP which caused a non-synonymous amino acid substitution. Genotypes of this SNP corresponded to the visual evaluation of root color in another breeding line. A chromoplast-specific lycopene β-cyclase (CYC-B) gene was a possible candidate for the β/α carotene ratio. On CYC-B, five amino acid substitutions were detected between parental plants of the F2 population. The detected associations and SNPs on the possible candidate genes will contribute to carrot breeding and the understanding of carotenoid biosynthesis and accumulation in orange carrots.

scholarly journals Genome-wide association study uncovers major genetic loci associated with seed flooding tolerance in soybean

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ripa Akter Sharmin ◽  
Benjamin Karikari ◽  
Fangguo Chang ◽  
G.M. Al Amin ◽  
Mashiur Rahman Bhuiyan ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Linear Model ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Mixed Linear Model ◽  
Genome Wide Association ◽  
Flooding Tolerance ◽  
Genome Wide ◽  
Germination Stage

Abstract Background Seed flooding stress is one of the threatening environmental stressors that adversely limits soybean at the germination stage across the globe. The knowledge on the genetic basis underlying seed-flooding tolerance is limited. Therefore, we performed a genome-wide association study (GWAS) using 34,718 single nucleotide polymorphism (SNPs) in a panel of 243 worldwide soybean collections to identify genetic loci linked to soybean seed flooding tolerance at the germination stage. Results In the present study, GWAS was performed with two contrasting models, Mixed Linear Model (MLM) and Multi-Locus Random-SNP-Effect Mixed Linear Model (mrMLM) to identify significant SNPs associated with electrical conductivity (EC), germination rate (GR), shoot length (ShL), and root length (RL) traits at germination stage in soybean. With MLM, a total of 20, 40, 4, and 9 SNPs associated with EC, GR, ShL and RL, respectively, whereas in the same order mrMLM detected 27, 17, 13, and 18 SNPs. Among these SNPs, two major SNPs, Gm_08_11971416, and Gm_08_46239716 were found to be consistently connected with seed-flooding tolerance related traits, namely EC and GR across two environments. We also detected two SNPs, Gm_05_1000479 and Gm_01_53535790 linked to ShL and RL, respectively. Based on Gene Ontology enrichment analysis, gene functional annotations, and protein-protein interaction network analysis, we predicted eight candidate genes and three hub genes within the regions of the four SNPs with Cis-elements in promoter regions which may be involved in seed-flooding tolerance in soybeans and these warrant further screening and functional validation. Conclusions Our findings demonstrate that GWAS based on high-density SNP markers is an efficient approach to dissect the genetic basis of complex traits and identify candidate genes in soybean. The trait associated SNPs could be used for genetic improvement in soybean breeding programs. The candidate genes could help researchers better understand the molecular mechanisms underlying seed-flooding stress tolerance in soybean.

scholarly journals Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Y. Tilahun ◽  
T. A. Gipson ◽  
T. Alexander ◽  
M. L. McCallum ◽  
P. R. Hoyt
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Predictive Power ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Breeding Value ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Dairy Traits

This paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single-nucleotide polymorphisms (SNP) BeadChip. The analysis used a polygenic model where the dropping criterion was a call rate≥0.95. The initial dataset was composed of ~60,000 rows of SNPs and 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50K BeadChip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provides precision breeding methods will thereby increase the breeding value.

scholarly journals Genome-Wide Association Study (GWAS) Reveals The Genetic Basis of Brace Root Angle and Diameter in Maize

2021 ◽  
Author(s):  
Daqiu Sun ◽  
Sibo Chen ◽  
Zhenhai Cui ◽  
Jingwei Lin ◽  
Meiling Liu ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Root Cells ◽  
Root Angle ◽  
Genome Wide ◽  
Wide Range ◽  
Significant Difference

Abstract Background:Brace roots are an important part of the maize root system. Among brace root traits, brace root angle (BRA) and brace root diameter (BRD) are important components that affect plant growth and development. However, there are no reports on the genetic basis of maize BRA and BRD. Results:Here, a genome-wide association study (GWAS) was conducted using 508 associated populations with extensive natural variation. The broad heritability of BRA and BRD reached 0.91 and 0.82, respectively. The analysis of different subgroups showed that there were significant differences in BRA traits in different subgroups, whereas there was no significant difference in BRD. Evaluation of phenotypic diversity in three different environments showed that BRA and BRD exhibit a wide range of natural variability. In the GWAS, the BRA and BRD were combined with 55,8629 single nucleotide polymorphisms, and four candidate genes were found for BRA within the threshold of P < 1.78×10-6 that were significantly related to BRD). These genes may (1) participate in maize brace root cell wall synthesis through cell transport (GRMZM2G479243); (2) involve hormone signaling pathways in the horizontal expansion of brace root cells (GRMZM2G101928 and GRMZM2G174736); or (3) involve the PLETHORA (PLT1/2) gene (GRMZM2G151934) to promote stem cells and transport expanded cells to affect the growth of root meristems.Conclusions:These results provide theoretical information for understanding the genetic basis of brace root development. Further research on candidate genes will help clarify the molecular pathways regulating BRA and BRD in maize.

scholarly journals Genome-Wide Association Analysis of Plant Height Using the Maize F1 Population

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 432 ◽  
Author(s):  
Zhang ◽  
Wan ◽  
He ◽  
Lan ◽  
Li
Keyword(s):  
Candidate Genes ◽  
Plant Height ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Plant Density ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Higher Plant ◽  
Genome Wide ◽  
A Genome

Drastic changes in plant height (PH) are observed when maize adapt to a higher plant density. Most importantly, PH is an important factor affecting maize yield. Although the genetic basis of PH has been extensively studied using different populations during the past decades, genetic basis remains unclear in the F1 population, which was a widely used population in production. In this study, a genome-wide association study (GWAS) was conducted using an F1 population consisting of 300 maize hybrids with 17,652 single nucleotide polymorphisms (SNPs) makers to identify candidate genes for controlling PH. A total of nine significant SNPs makers and two candidate genes were identified for PH. The candidate genes, Zm00001d018617 and Zm00001d023659, were the genes most probable to be involved in the development of PH. Our results provide new insights into the genetic basis of PH in maize.

scholarly journals Genome-wide association study reveals the genetic basis of yield- and quality-related traits in wheat

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Le Gao ◽  
Chengsheng Meng ◽  
Tengfei Yi ◽  
Ke Xu ◽  
Huiwen Cao ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Wheat Yield ◽  
Significant Snps ◽  
Wheat Breeding ◽  
Genome Wide Association ◽  
Yield And Quality ◽  
Genome Wide

Abstract Background Identifying the loci and dissecting the genetic architecture underlying wheat yield- and quality-related traits are essential for wheat breeding. A genome-wide association study was conducted using a high-density 90 K SNP array to analyze the yield- and quality-related traits of 543 bread wheat varieties. Results A total of 11,140 polymorphic SNPs were distributed on 21 chromosomes, including 270 significant SNPs associated with 25 yield- and quality-related traits. Additionally, 638 putative candidate genes were detected near the significant SNPs based on BLUP data, including three (TraesCS7A01G482000, TraesCS4B01G343700, and TraesCS6B01G295400) related to spikelet number per spike, diameter of the first internode, and grain volume. The three candidate genes were further analyzed using stage- and tissue- specific gene expression data derived from an RNA-seq analysis. These genes are promising candidates for enhancing yield- and quality-related traits in wheat. Conclusions The results of this study provide a new insight to understand the genetic basis of wheat yield and quality. Furthermore, the markers detected in this study may be applicable for marker-assisted selection in wheat breeding programs.

scholarly journals A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

2020 ◽  
Author(s):  
Alkesh Hada ◽  
Tushar K. Dutta ◽  
Nisha Singh ◽  
Vandna Rai ◽  
Nagendra K. Singh ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Wild Rice ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Root Knot Nematode ◽  
Meloidogyne Graminicola ◽  
Genome Wide ◽  
A Genome

Abstract Background: Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. Results: We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K “OsSNPnks” genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. Conclusion: The identified SNPs enrich the repository of candidate genes for future marker-assisted breeding program to alleviate the damage of RRKN in rice.

scholarly journals Genome-wide association study (GWAS) with productivity in Romanov sheep breed

2021 ◽  
Vol 59 (1) ◽  
pp. 71-80
Author(s):  
A. Y. Krivoruchko ◽  
O. A. Yatsyk ◽  
T. Y. Saprikina ◽  
D. D. Petukhova
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Elite Group ◽  
Genome Wide ◽  
Productive Traits

Genetic technologies used in breeding of small ruminants requires searching for new molecular markers of productive traits. The most effective for this is genome-wide association study (GWAS) of single nucleotide polymorphisms (SNP) with economically valuable traits. The paper presents results of study of associations of the frequency of single nucleotide polymorphisms with a rank assessment according to complex of productive traits (super-elite) in Romanov sheep using DNA biochips Ovine Infinium HD BeadChip 600K. Eleven SNPs have been found having significant correlation with the animals belonging to the “super-elite” group. Five substitutions are located in the genes introns, six are related to intergenic polymorphisms. The highest reliability of association with productivity was observed in substitution rs410516628 (р = 3,14 · 10-9) located on the 3rd chromosome. Substitution rs422028000 on 2nd chromosome differs with the fact that in the “super-elite” group it was found in 90 % of haplotypes. Polymorphisms rs411162754 (1st chromosome) and rs417281100 (10th chromosome) in our study turned out to be the rarest – only in “super-elite” group and only in a quarter of haplotypes. The genes located near the identified SNPs are mainly associated with metabolic and regulatory processes. Our study has identified several new candidate genes with polymorphism probably associated with the ranking in terms of productivity in Romanov sheep: LTBP1, KCNH8, LMX1B, ZBTB43, MSRA, CHPF, PID1 and DNER. The results obtained create a theoretical basis for further study of candidate genes affecting implementation of phenotypic traits in Romanov sheep. The revealed polymorphisms associated with the productive traits of sheep can be used in practical breeding as molecular and genetic markers for selection of parental pairs.

scholarly journals Dissection of the Genetic Basis of Rice Panicle Architecture Using a Genome-wide Association Study

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Shaoxing Bai ◽  
Jun Hong ◽  
Ling Li ◽  
Su Su ◽  
Zhikang Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Association Study ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Panicle Length ◽  
Genome Wide ◽  
A Genome ◽  
Panicle Architecture

AbstractPanicle architecture is one of the major factors influencing productivity of rice crops. The regulatory mechanisms underlying this complex trait are still unclear and genetic resources for rice breeders to improve panicle architecture are limited. Here, we have performed a genome-wide association study (GWAS) to analyze and identify genetic determinants underlying three panicle architecture traits. A population of 340 rice accessions from the 3000 Rice Genomes Project was phenotyped for panicle length, primary panicle number and secondary branch number over two years; GWAS was performed across the whole panel, and also across the japonica and indica sub-panels. A total of 153 quantitative trait loci (QTLs) were detected, of which 5 were associated with multiple traits, 8 were unique to either indica or japonica sub-panels, while 37 QTLs were stable across both years. Using haplotype and expression analysis, we reveal that genetic variations in the OsSPL18 promoter significantly affect gene expression and correlate with panicle length phenotypes. Three new candidate genes with putative roles in determining panicle length were also identified. Haplotype analysis of OsGRRP and LOC_Os03g03480 revealed high association with panicle length variation. Gene expression of DSM2, involved in abscisic acid biosynthesis, was up-regulated in long panicle accessions. Our results provide valuable information and resources for further unravelling the genetic basis determining rice panicle architecture. Identified candidate genes and molecular markers can be used in marker-assisted selection to improve rice panicle architecture through molecular breeding.

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