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 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.

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 Mining candidate gene for rice aluminum tolerance through genome wide association study and transcriptomic analysis

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Peng Zhang ◽  
Kaizhen Zhong ◽  
Zhengzheng Zhong ◽  
Hanhua Tong
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Core Collection ◽  
Genome Wide Association Study ◽  
High Rate ◽  
Genome Wide Association ◽  
Genetic Mechanism ◽  
Al Tolerance ◽  
Genome Wide ◽  
Significant Difference

Abstract Background The genetic mechanism of aluminum (Al) tolerance in rice is great complicated. Uncovering genetic mechanism of Al tolerance in rice is the premise for Al tolerance improvement. Mining elite genes within rice landrace is of importance for improvement of Al tolerance in rice. Results Genome-wide association study (GWAS) performed in EMMAX for rice Al tolerance was carried out using 150 varieties of Ting’s core collection constructed from 2262 Ting’s collections with more than 3.8 million SNPs. Within Ting’s core collection of clear population structure and kinship relatedness as well as high rate of linkage disequilibrium (LD) decay, 17 genes relating to rice Al tolerance including cloned genes like NRAT1, ART1 and STAR1 were identified in this study. Moreover, 13 new candidate regions with high LD and 69 new candidate genes were detected. Furthermore, 20 of 69 new candidate genes were detected with significant difference between Al treatment and without Al toxicity by transcriptome sequencing. Interestingly, both qRT-PCR and sequence analysis in CDS region demonstrated that the candidate genes in present study might play important roles in rice Al tolerance. Conclusions The present study provided important information for further using these elite genes existing in Ting’s core collection for improvement of rice Al tolerance.

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 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.

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 Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 718
Author(s):  
Bingxin Meng ◽  
Tao Wang ◽  
Yi Luo ◽  
Deze Xu ◽  
Lanzhi Li ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Association Analysis ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Genome Wide Association ◽  
Lodging Resistance ◽  
Leaf Type ◽  
Stem Strength ◽  
Genome Wide

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

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