scholarly journals Fine Mapping and Candidate Gene Analysis of a Major Locus Controlling Ovule Abortion and Seed Number Per Silique in Brassica Napus L.

2021 ◽  
Author(s):  
Yangmiao Jiao ◽  
Kunpeng Zhang ◽  
Guangqin Cai ◽  
Kaidi Yu ◽  
Olalekan Amoo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Fine Mapping ◽  
Developmental Process ◽  
Seed Number ◽  
Brassica Napus L ◽  
Dh Population ◽  
Ovule Abortion ◽  
Ovule Number ◽  
Trait Locus ◽  
Silique Length

Abstract Key message A major QTL controlling ovule abortion and SN was fine-mapped to a 80.1-kb region on A8 in rapeseed, and BnaA08g07940D and BnaA08g07950D are the most likely candidate genes.Abstact The seed number per silique (SN), an important yield determining trait of rapeseed, is the final consequence of a complex developmental process including ovule initiation and the subsequent ovule/seed development. To elucidate the genetic mechanism regulating the natural variation of SN and its related components, quantitative trait locus (QTL) mapping was conducted using a doubled haploid (DH) population derived from the cross between C4-146 and C4-58B, which showed significant differences in SN and aborted ovule number (AON), but no obvious differences in ovule number (ON). QTL analysis identified 19 consensus QTLs for six SN-related traits across three environments. A novel QTL on chromosome A8, un.A8, which pleiotropically controls all these traits except for ON, was stably detected across the three environments.This QTL explained more than 50% of the SN, AON and percentage of aborted ovule (PAO) variations as well as a moderate contribution on silique length (SL) and thousand seed weight (TSW). The C4-146 allele at the locus increases SN and SL but decreases AON, PAO and TSW. Further fine mapping narrowed down this locus into a 80.1-kb interval flanked by markers BM1668 and BM1672, and six predicted genes were annotated in the delimited region. Expression analyses and DNA sequencing showed that two homologs of Arabidopsis photosystem I subunit F (BnaA08g07940D) and zinc transporter 10 precursor (BnaA08g07950D) were the most promising candidate genes underlying this locus. These results provide a solid basis for cloning un.A8 to reduce the ovule abortion and increase SN in the yield improvement of rapeseed.

scholarly journals QTL Analysis of Five Silique-Related Traits in Brassica napus L. Across Multiple Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaozhen Zhao ◽  
Kunjiang Yu ◽  
Chengke Pang ◽  
Xu Wu ◽  
Rui Shi ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Networks ◽  
Reproductive Organ ◽  
High Yield ◽  
Potential Candidate ◽  
Seed Number ◽  
Brassica Napus L ◽  
Functional Annotations ◽  
Multiple Environments ◽  
Silique Length

As an important physiological and reproductive organ, the silique is a determining factor of seed yield and a breeding target trait in rapeseed (Brassica napus L.). Genetic studies of silique-related traits are helpful for rapeseed marker-assisted high-yield breeding. In this study, a recombinant inbred population containing 189 lines was used to perform a quantitative trait loci (QTLs) analysis for five silique-related traits in seven different environments. As a result, 120 consensus QTLs related to five silique-related traits were identified, including 23 for silique length, 25 for silique breadth, 29 for silique thickness, 22 for seed number per silique and 21 for silique volume, which covered all the chromosomes, except C5. Among them, 13 consensus QTLs, one, five, two, four and one for silique length, silique breadth, silique thickness, seed number per silique and silique volume, respectively, were repeatedly detected in multiple environments and explained 4.38–13.0% of the phenotypic variation. On the basis of the functional annotations of Arabidopsis homologous genes and previously reported silique-related genes, 12 potential candidate genes underlying these 13 QTLs were screened and found to be stable in multiple environments by analyzing the re-sequencing results of the two parental lines. These findings provide new insights into the gene networks affecting silique-related traits at the QTL level in rapeseed.

scholarly journals Fine Mapping of a Locus Underlying the Ectopic Blade-Like Outgrowths on Leaf and Screening Its Candidate Genes in Rapeseed (Brassica napus L.)

2021 ◽  
Vol 11 ◽  
Author(s):  
Liang Chai ◽  
Bin Feng ◽  
Xun Liu ◽  
Liangcai Jiang ◽  
Shu Yuan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Fine Mapping ◽  
Higher Plants ◽  
Bulked Segregant Analysis ◽  
Amplification Refractory Mutation System ◽  
Adaxial Side ◽  
Brassica Napus L ◽  
Index Method ◽  
Leaf Formation ◽  
Mutation System

Leaf is an important organ for higher plants, and the shape of it is one of the crucial traits of crops. In this study, we investigated a unique aberrant leaf morphology trait in a mutational rapeseed material, which displayed ectopic blade-like outgrowths on the adaxial side of leaf. The abnormal line 132000B-3 was crossed with the normal line 827-3. Based on the F2:3 family, we constructed two DNA pools (normal pool and abnormal pool) by the bulked segregant analysis (BSA) method and performed whole genome re-sequencing (WGR), obtaining the single-nucleotide polymorphism (SNP) and insertion/deletion (InDel) data. The SNP-index method was used to calculate the Δ(SNP/InDel-index), and then an association region was identified on chromosome A10 with a length of 5.5 Mbp, harboring 1048 genes totally. Subsequently, the fine mapping was conducted by using the penta-primer amplification refractory mutation system (PARMS), and the associated region was narrowed down to a 35.1-kbp segment, containing only seven genes. These seven genes were then analyzed according to their annotations and finally, BnA10g0422620 and BnA10g0422610, orthologs of LATE MERISTEM IDENTITY1 (LMI1) gene from Arabidopsis and REDUCED COMPLEXITY (RCO) gene from its relative Cardamine hirsuta, respectively, were identified as the candidate genes responding to this blade-like outgrowth trait in rapeseed. This study provides a novel perspective into the leaf formation in Brassica plants.

scholarly journals Expression Profile And Genome-Wide Association Analyze of Silique Length In Brassica Napus L.

2021 ◽  
Author(s):  
Jia wang ◽  
Yueling Fan ◽  
Lin Mao ◽  
Cunmin Qu ◽  
Kun Lu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Candidate Genes ◽  
Lignin Content ◽  
Signal Transmission ◽  
Sucrose Metabolism ◽  
Brassica Napus L ◽  
Genome Wide ◽  
Phenylpropanoid Biosynthesis ◽  
Important Trait ◽  
Silique Length

Abstract Background: Silique length (SL) is an important trait tightly related to seed yield in Brassica napus (B. napus). Many studies related to SL have been reported in B. napus, but only a few candidate genes have been found and cloned, and the regulatory mechanism of SL is not clear. Results: We identified QTL for SL by using a RIL population and two independent GWAS populations. Major QTL on A07, A09, and C08 chromosome were stably detected in all environments from all populations. As important candidate genes, several genes related to starch and sucrose metabolism, plant hormone signal transmission and phenylpropanoid biosynthesis were detected in the main QTL interval. Such as, BnaA9.CP12-2, BnaA9.NST2, BnaA7.MYB63, BnaA7.ARF17, etc. At the same time, the results of RNA-seq and WGCNA showed that starch and sucrose metabolism, photosynthesis, and secondary cell wall biosynthesis played an important role in the development of siliques. Conclusions: we propose that photosynthesis, sucrose and starch metabolism, plant hormones, and lignin content play an important role in the development of rapeseed silique.

scholarly journals Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xingyi Wang ◽  
Hui Liu ◽  
Kadambot H. M. Siddique ◽  
Guijun Yan
Keyword(s):  
Candidate Genes ◽  
Quantitative Trait ◽  
Genomic Region ◽  
Nucleotide Polymorphisms ◽  
Near Isogenic Lines ◽  
Gene Effects ◽  
Isogenic Lines ◽  
Trait Locus ◽  
Grain Yield And Quality ◽  
Sprouting Resistance

Abstract Background Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL) QPhs.ccsu-3A.1 for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated. Results Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlie QPhs.ccsu-3A.1 responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines. Conclusions The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.

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