A genome-wide association study of plant height and primary branch number in rapeseed ( Brassica napus )

Plant Science ◽  
2016 ◽  
Vol 242 ◽  
pp. 169-177 ◽  
Author(s):  
Feng Li ◽  
Biyun Chen ◽  
Kun Xu ◽  
Guizhen Gao ◽  
Guixin Yan ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Association Study ◽  
Plant Height ◽  
Genome Wide Association Study ◽  
Primary Branch ◽  
Genome Wide Association ◽  
Branch Number ◽  
Genome Wide ◽  
A Genome

Genome‑wide association study dissects the genetic control of plant height and branch number in response to low‑phosphorus stress in Brassica napus

2021 ◽  
Author(s):  
Haijiang Liu ◽  
Jingchi Wang ◽  
Bingbing Zhang ◽  
Xinyu Yang ◽  
John P Hammond ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Association Study ◽  
Candidate Genes ◽  
Plant Height ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Branch Number ◽  
P Deficiency ◽  
Genome Wide ◽  
P Supply

Abstract Background and Aims Oilseed rape (Brassica napus) is one of the most important oil crops worldwide. Phosphorus (P) deficiency severely decreases the plant height (PH) and branch number (BN) of B. napus. However, the genetic bases controlling PH and BN in B. napus under P deficiency remain largely unknown. This study aims to mine candidate genes for PH and BN by genome-wide association study (GWAS) and determine low-P tolerance haplotypes. Methods An association panel of B. napus were grown in the field with a low P supply (P, 0 kg/ha) and a sufficient P supply (P, 40 kg/ha) across two years and PH and BN were investigated. More than five million single-nucleotide polymorphisms (SNPs) were used to conduct GWAS of PH and BN at two contrasting P supplies. Key Results A total of 2127 SNPs were strongly associated (P < 6.25×10 −07) with PH and BN at two P supplies. There was significant correlation between phenotypic variation and the number of favorable alleles of associated loci on chromosomes A10 (chrA10_821671) and C08 (chrC08_27999846), which will contribute to breeding improvement by aggregating these SNPs. BnaA10g09290D and BnaC08g26640D were identified to be associated with the chrA10_821671 and chrC08_27999846, respectively. Candidate gene association analysis and haplotype analysis showed that the inbred lines carrying ATT at 'BnaA10g09290Hap1' and AAT at 'BnaC08g26640Hap1' had higher PH than lines carrying other haplotype alleles at low P supply. Conclusion Our results demonstrate the power of GWAS in identifying genes of interest in B. napus and provided insights into the genetic basis of PH and BN at low P supply in B. napus. Candidate genes and favorable haplotypes may facilitate marker-based breeding efforts aimed at improving P use efficiency in B. napus.

scholarly journals Genome wide association study of plant height and tiller number in hulless barley

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260723
Author(s):  
Yixiong Bai ◽  
Xiaohong Zhao ◽  
Xiaohua Yao ◽  
Youhua Yao ◽  
Likun An ◽  
...  
Keyword(s):  
Association Study ◽  
Plant Height ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Tiller Number ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Hulless Barley ◽  
Genome Wide ◽  
A Genome

Hulless barley (Hordeum vulgare L. var. nudum), also called naked barley, is a unique variety of cultivated barley. The genome-wide specific length amplified fragment sequencing (SLAF-seq) method is a rapid deep sequencing technology that is used for the selection and identification of genetic loci or markers. In this study, we collected 300 hulless barley accessions and used the SLAF-seq method to identify candidate genes involved in plant height (PH) and tiller number (TN). We obtained a total of 1407 M paired-end reads, and 228,227 SLAF tags were developed. After filtering using an integrity threshold of >0.8 and a minor allele frequency of >0.05, 14,504,892 single-nucleotide polymorphisms (SNP) loci were screened out. The remaining SNPs were used for the construction of a neighbour-joining phylogenetic tree, and the three subcluster members showed no obvious differentiation among regional varieties. We used a genome wide association study approach to identify 1006 and 113 SNPs associated with TN and PH, respectively. Based on best linear unbiased predictors (BLUP), 41 and 29 SNPs associated with TN and PH, respectively. Thus, several of genes, including Hd3a and CKX5, may be useful candidates for the future genetic breeding of hulless barley. Taken together, our results provide insight into the molecular mechanisms controlling barley architecture, which is important for breeding and yield.

scholarly journals Genome-Wide Association Study Identified Novel Genomic Loci Controlling Internode Lengths and Plant Height in Common Wheat under Different Nitrogen Treatments

2021 ◽  
Author(s):  
Piyi Xing ◽  
Xia Zhang ◽  
Dandan Li ◽  
Honggang Wang ◽  
Yinguang Bao ◽  
...  
Keyword(s):  
Association Study ◽  
Plant Height ◽  
Genome Wide Association Study ◽  
Nitrogen Deficiency ◽  
Internode Length ◽  
Spike Length ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Low Nitrogen

Abstract Nitrogen is an important nutrient for crop growth and development. Plant height-related traits can be affected by nitrogen supplementation. In this study, we performed a genome-wide association study (GWAS) on plant height, spike length, length of different internodes, and lodging resistance strength at the grain-filling stage based on a natural wheat population subjected to low nitrogen and normal (CK) treatments. GWAS analysis showed that a total of 86 quantitative trait locus (QTLs) were detected, including 13 QTLs for plant height, 10 QTLs for spike length, 19 QTLs for the length of the first internode from the top of the plant, 6 QTLs for the second internode length, 11 QTLs for the third internode length, 13 QTLs for the fourth internode length, and 14 QTLs for the fifth internode length. Compared to the CK treatment, the plant height, spike length, and fourth and fifth internode lengths were significantly affected by the low nitrogen treatment. A total of 18 QTLs responding to low nitrogen stress were detected, including three QTLs for the fourth internode length detected on 3A, 6A, and 6D chromosomes, eleven QTLs for the fifth internode length on 1A, 1B, 1D, 2A, 2B, 3A, 3B, 4A, 5B and 7B chromosomes, one QTL for spike length on 3A chromosome, and one QTL for plant height on 5B chromosome. These QTLs will enhance our understanding of the genetic basis of plant height responses to nitrogen deficiency and will benefit genetic reactions to nitrogen fertilization.

scholarly journals Genome-wide association study and genomic selection for yield and related traits in soybean

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255761
Author(s):  
Waltram Ravelombola ◽  
Jun Qin ◽  
Ainong Shi ◽  
Qijian Song ◽  
Jin Yuan ◽  
...  
Keyword(s):  
Association Study ◽  
Genomic Selection ◽  
Plant Height ◽  
Seed Weight ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Soybean [Glycine max (L.) Merr.] is a crop of great interest worldwide. Exploring molecular approaches to increase yield genetic gain has been one of the main challenges for soybean breeders and geneticists. Agronomic traits such as maturity, plant height, and seed weight have been found to contribute to yield. In this study, a total of 250 soybean accessions were genotyped with 10,259 high-quality SNPs postulated from genotyping by sequencing (GBS) and evaluated for grain yield, maturity, plant height, and seed weight over three years. A genome-wide association study (GWAS) was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model. Genomic selection (GS) was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that 20, 31, 37, and 23 SNPs were significantly associated with maturity, plant height, seed weight, and yield, respectively; Many SNPs were mapped to previously described maturity and plant height loci (E2, E4, and Dt1) and a new plant height locus was mapped to chromosome 20. Candidate genes were found in the vicinity of the two SNPs with the highest significant levels associated with yield, maturity, plant height, seed weight, respectively. A 11.5-Mb region of chromosome 10 was associated with both yield and seed weight. Overall, the accuracy of GS was dependent on the trait, year, and population structure, and high accuracy indicates that these agronomic traits can be selected in molecular breeding through GS. The SNP markers identified in this study can be used to improve yield and agronomic traits through the marker-assisted selection and GS in breeding programs.

scholarly journals A combination of genome-wide association study and transcriptome analysis in leaf epidermis identifies candidate genes involved in cuticular wax biosynthesis in Brassica napus

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Shurong Jin ◽  
Shuangjuan Zhang ◽  
Yuhua Liu ◽  
Youwei Jiang ◽  
Yanmei Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Association Study ◽  
Stress Tolerance ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Cuticular Waxes ◽  
Biochemical Basis ◽  
Genome Wide ◽  
A Genome ◽  
Wax Load

Abstract Background Brassica napus L. is one of the most important oil crops in the world. However, climate-change-induced environmental stresses negatively impact on its yield and quality. Cuticular waxes are known to protect plants from various abiotic/biotic stresses. Dissecting the genetic and biochemical basis underlying cuticular waxes is important to breed cultivars with improved stress tolerance. Results Here a genome-wide association study (GWAS) of 192 B. napus cultivars and inbred lines was used to identify single-nucleotide polymorphisms (SNPs) associated with leaf waxes. A total of 202 SNPs was found to be significantly associated with 31 wax traits including total wax coverage and the amounts of wax classes and wax compounds. Next, epidermal peels from leaves of both high-wax load (HW) and low-wax load (LW) lines were isolated and used to analyze transcript profiles of all GWAS-identified genes. Consequently, 147 SNPs were revealed to have differential expressions between HW and LW lines, among which 344 SNP corresponding genes exhibited up-regulated while 448 exhibited down-regulated expressions in LW when compared to those in HW. According to the gene annotation information, some differentially expressed genes were classified into plant acyl lipid metabolism, including fatty acid-related pathways, wax and cutin biosynthesis pathway and wax secretion. Some genes involved in cell wall formation and stress responses have also been identified. Conclusions Combination of GWAS with transcriptomic analysis revealed a number of directly or indirectly wax-related genes and their associated SNPs. These results could provide clues for further validation of SNPs for marker-assisted breeding and provide new insights into the genetic control of wax biosynthesis and improving stress tolerance of B. napus.

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