Genome-wide association studies in the genetic dissection of ovule number, seed number, and seed weight in Brassica napus L.

Khan, Shahid Ullah; Jiao, Yangmiao; Liu, Sheng; Zhang, Xiaoying; Khan, Muhammad Hafeez Ullah; Zhai, Yungu; Amoo, Olalekan; Fan, Chuchuan; Zhou, Yongming

doi:10.1016/j.indcrop.2019.111877

Cited by 42 publications

(59 citation statements)

References 84 publications

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“…Rapeseed ( Brassica napus L., AACC, 2 n = 38), is an important crop grown all over the world, providing approximately 16% of the entire global edible vegetable oils for human diets as well as high‐quality animal feed proteins and raw materials for industrial processes (Hu et al, 2018; S. U. Khan et al, 2019). It resulted from a recent allopolyploidy between ancestors of Brassica rapa (2 n = 20, AA) and Brassica oleracea (2 n = 18, CC).…”

Section: Introductionmentioning

confidence: 99%

Targeted mutagenesis of EOD3 gene in Brassica napus L. regulates seed production

Khan

Zhu

et al. 2020

Journal Cellular Physiology

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Seed size and number are central to the evolutionary fitness of plants and are also crucial for seed production of crops. However, the molecular mechanisms of seed production control are poorly understood in Brassica crops. Here, we report the gene cloning, expression analysis, and functional characterization of the EOD3/CYP78A6 gene in rapeseed. BnaEOD3 has four copies located in two subgenomes, which exhibited a steady higher expression during seed development with differential expression among copies. The targeted mutations of BnaEOD3 gene were efficiently generated by stable transformation of the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat) vector. These mutations were stably transmitted to T 1 and T 2 generations and a large collection of homozygous mutants with combined loss-of-function alleles across four BnaEOD3 copies were created for phenotyping. All mutant T 1 lines had shorter siliques, smaller seeds, and an increased number of seeds per silique, in which the quadrable mutants showed the most significant changes in these traits. Consequently, the seed weight per plant in the quadrable mutants increased by 13.9% on average compared with that of wild type, indicating that these BnaEOD3 copies have redundant functions in seed development in rapeseed. The phenotypes of the different allelic combinations of BnaEOD3 copies also revealed gene functional differentiation among the two subgenomes. Cytological observations indicated that the BnaEOD3 could act maternally to promote cotyledon cell expansion and proliferation to regulate seed growth in rapeseed. Collectively, our findings reveal the quantitative involvement of the different BnaEOD3 copies function in seed development, but also provided valuable resources for rapeseed breeding programs.

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Section: Introductionmentioning

confidence: 99%

Targeted mutagenesis of EOD3 gene in Brassica napus L. regulates seed production

Khan

Zhu

et al. 2020

Journal Cellular Physiology

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“…Furthermore, 19 SNPs co-detected by using ML-GWAS and SL-GWAS methods together (Additional le 5). A comparison of the four ML-GWAS methods revealed that pLARmEB was more powerful and robust [68], than the other three models in the detection signi cant SNPs for plant architectural traits. Through integrating the results of four ML-GWAS and three SL-GAWS methods led to the veri cation of the signi cance of ML-GWAS models.…”

Section: Signi Cance Of Gwas Using High-density Genotypingmentioning

confidence: 99%

“…With the advent of molecular markers and genome studies, several association mapping approaches have been developed to reveal the genetic architecture of complex traits in crops [68,69]. In earlier studies, mostly SL-GWAS methods were adopted to dissect complex traits, but only few SNPs for each trait have been identi ed due to its procedural limitations.…”

Section: Signi Cance Of Gwas Using High-density Genotypingmentioning

confidence: 99%

“…The combination of two SL-GWAS and ML-GWAS methods contributes e ciently to detection of signi cant loci associated with pre-harvest sprouting tolerance in wheat [77]. SU Khan, J Yangmiao, S Liu, K Zhang, MHU Khan, Y Zhai, A Olalekan, C Fan and Y Zhou [68] combined SL and ML-GWAS approaches and revealed that ML-GWAS methods are more effective with high robustness and power of QTN detection than SL-GWAS in the genetic dissection of yield related traits of rapeseed genotypes. Li and his co-workers integrated the results of three single locus GWAS and three multi locus methods for ber quality traits in upland cotton [78].…”

Section: Signi Cance Of Gwas Using High-density Genotypingmentioning

confidence: 99%

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Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using GWAS

Wang¹,

Ali²,

Hu³

et al. 2020

Preprint

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Background: Wheat is a staple food crop worldwide. Plant height is a key factor in plant architecture as it plays a crucial role in lodging and thus affects yield and quality. Genome-wide studies are mostly applied in crop plants, due to its advanced genotyping technologies, identification of novel loci, and improved statistical approaches. Results: In this study, the population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by four ML-GWAS and three SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were commonly detected, including seven across multiple environments and thirty-six across multiple methods. Interestingly, five most stable SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, possibly played a role in modulating plant height and flag leaf length. When comparing ML-GWAS methods, pLARmEB was the most powerful and accountable for the detection of 49 significant SNPs that mostly contributed to plant height (36 SNPs). However, in SL-GWAS the FarmCPU model detected most of the significant SNPs. Moreover, a total of 152 candidate genes were found that are likely to be involved in plant growth and development which may provide insightful information related to plant architectural traits.Conclusion: Altogether, our results reveal 174 and 97 significant SNPs controlling plant architectural traits using four ML-GWAS and three SL-GWAS methods, respectively. The detection of the stable loci across multiple environments and methods, possibly play a role in modulating plant architectural traits in hexaploid wheat, and finally will contribute to the discovery of valuable SNP loci for marker-assisted selection (MAS) in wheat molecular breeding.

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“…Rapeseed (Brassica napus) is the second most important oilseed crop in the world, providing edible oil and raw material for bio-energy applications [1]. China is the second-largest producer of rapeseed, which is the fourth-largest crop in this country after rice, wheat, and maize [2].…”

Section: Introductionmentioning

confidence: 99%

CRb and PbBa8.1 Synergically Increases Resistant Genes Expression upon Infection of Plasmodiophora brassicae in Brassica napus

Shah

et al. 2020

Genes

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PbBa8.1 and CRb are two clubroot-resistant genes that are important for canola breeding in China. Previously, we combined these resistant genes and developed a pyramid-based, homozygous recurrent inbred line (618R), the results of which showed strong resistance to Plasmodiophora brassicae field isolates; however, the genetic mechanisms of resistance were unclear. In the present work, we conducted comparative RNA sequencing (RNA-Seq) analysis between 618R and its parental lines (305R and 409R) in order to uncover the transcriptomic response of the superior defense mechanisms of 618R and to determine how these two different resistant genes coordinate with each other. Here, we elucidated that the number and expression of differentially expressed genes (DEGs) in 618R are significantly higher than in the parental lines, and PbBa8.1 shares more DEGs and plays a dominant role in the pyramided line. The common DEGs among the lines largely exhibit non-additive expression patterns and enrichment in resistance pathways. Among the enriched pathways, plant–pathogen interaction, plant hormone signaling transduction, and secondary metabolites are the key observation. However, the expressions of the salicylic acid (SA) signaling pathway and reactive oxygen species (ROS) appear to be crucial regulatory components in defense response. Our findings provide comprehensive transcriptomic insight into understanding the interactions of resistance gene pyramids in single lines and can facilitate the breeding of improved resistance in Brassica napus.

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Genome-wide association studies in the genetic dissection of ovule number, seed number, and seed weight in Brassica napus L.

Cited by 42 publications

References 84 publications

Targeted mutagenesis of EOD3 gene in Brassica napus L. regulates seed production

Targeted mutagenesis of EOD3 gene in Brassica napus L. regulates seed production

Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using GWAS

CRb and PbBa8.1 Synergically Increases Resistant Genes Expression upon Infection of Plasmodiophora brassicae in Brassica napus

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