QTL Mapping and Diurnal Transcriptome Analysis Identify Candidate Genes Regulating Brassica napus Flowering Time

Timely flowering is important for seed formation and maximization of rapeseed (Brassica napus) yield. Here, we performed flowering-time quantitative trait loci (QTL) mapping using a double haploid (DH) population grown in three environments to study the genetic architecture. Brassica 60 K Illumina Infinium™ single nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers were used for genotyping of the DH population, and a high-density genetic linkage map was constructed. QTL analysis of flowering time from the three environments revealed five consensus QTLs, including two major QTLs. A major QTL located on chromosome A03 was detected specifically in the semi-winter rapeseed growing region, and the one on chromosome C08 was detected in all environments. Ribonucleic acid sequencing (RNA-seq) was performed on the parents’ leaves at seven time-points in a day to determine differentially expressed genes (DEGs). The biological processes and pathways with significant enrichment of DEGs were obtained. The DEGs in the QTL intervals were analyzed, and four flowering time-related candidate genes were found. These results lay a foundation for the genetic regulation of rapeseed flowering time and create a rapeseed gene expression library for seven time-points in a day.

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Candidate genes screening for plant height and the first branch height based on QTL mapping and genome-wide association study in rapessed (<italic>Brassica napus</italic> L.)

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2020.94067 ◽

2019 ◽

Vol 46 (2) ◽

pp. 214-227

Author(s):

Cun-Min QU ◽

Jia-Na LI ◽

Zhi-You CHEN ◽

Kun LU ◽

Qiang HUO ◽

...

Keyword(s):

Brassica Napus ◽

Qtl Mapping ◽

Association Study ◽

Candidate Genes ◽

Plant Height ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

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Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L

BMC Genomics ◽

10.1186/s12864-018-5356-8 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 11

Author(s):

Hongju Jian ◽

Aoxiang Zhang ◽

Jinqi Ma ◽

Tengyue Wang ◽

Bo Yang ◽

...

Keyword(s):

Brassica Napus ◽

Qtl Mapping ◽

Flowering Time ◽

Transcriptome Sequencing ◽

Sequencing Analysis ◽

Brassica Napus L

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Combined QTL mapping, physiological and transcriptomic analyses to identify candidate genes involved in Brassica napus seed aging

Molecular Genetics and Genomics ◽

10.1007/s00438-018-1468-8 ◽

2018 ◽

Vol 293 (6) ◽

pp. 1421-1435 ◽

Cited By ~ 5

Author(s):

Tengyue Wang ◽

Lintao Hou ◽

Hongju Jian ◽

Feifei Di ◽

Jiana Li ◽

...

Keyword(s):

Brassica Napus ◽

Qtl Mapping ◽

Candidate Genes ◽

Seed Aging

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QTL Mapping for Seedling Dry Weight and Fresh Weight under Salt Stress and Candidate Genes Analysis in Brassica napus L.

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2017.00179 ◽

2017 ◽

Vol 43 (2) ◽

pp. 179

Author(s):

Lin-Tao HOU ◽

Teng-Yue WANG ◽

Hong-Ju JIAN ◽

Jia WANG ◽

Jia-Na LI ◽

...

Keyword(s):

Salt Stress ◽

Brassica Napus ◽

Qtl Mapping ◽

Candidate Genes ◽

Dry Weight ◽

Fresh Weight ◽

Brassica Napus L

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Combined QTL mapping and association study reveals candidate genes for leaf number and flowering time in maize

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03907-x ◽

2021 ◽

Author(s):

Zhigang Li ◽

Kun Li ◽

Xiaohong Yang ◽

Huaiqing Hao ◽

Hai-Chun Jing

Keyword(s):

Qtl Mapping ◽

Association Study ◽

Flowering Time ◽

Candidate Genes ◽

Leaf Number

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SEED COLOUR IN BRASSICA NAPUS: QTL MAPPING, CANDIDATE GENES AND ASSOCIATIONS WITH QUALITY TRAITS

Acta Horticulturae ◽

10.17660/actahortic.2006.706.24 ◽

2006 ◽

pp. 203-210 ◽

Cited By ~ 3

Author(s):

A.G. Badani ◽

B. Wittkop ◽

W. Lühs ◽

R. Baetzel ◽

R. Horn ◽

...

Keyword(s):

Brassica Napus ◽

Qtl Mapping ◽

Candidate Genes ◽

Quality Traits ◽

Seed Colour

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Inheritance Analysis and Quantitative Trait Loci Detection of Head Splitting Resistance in Cabbage (Brassica oleracea L. var. capitata)

HortScience ◽

10.21273/hortsci.50.7.944 ◽

2015 ◽

Vol 50 (7) ◽

pp. 944-951 ◽

Cited By ~ 1

Author(s):

Yanbin Su ◽

Yumei Liu ◽

Huolin Shen ◽

Xingguo Xiao ◽

Zhansheng Li ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Qtl Mapping ◽

Quantitative Trait ◽

Major Gene ◽

Genetic Regulation ◽

Interval Mapping ◽

Phenotypic Data ◽

Dh Population ◽

Trait Loci ◽

Inclusive Composite Interval Mapping

Head splitting resistance (HSR) in cabbage is an important trait closely related to appearance, yield, storability, and mechanical harvestability. In this study, a doubled haploid (DH) population derived from a cross between head splitting-susceptible inbred cabbage line 79-156 and resistant line 96-100 was used to analyze inheritance and detect quantitative trait loci (QTLs) for HSR during 2011–12 in Beijing, China. The analysis was performed using a mixed major gene/polygene inheritance method and QTL mapping. This approach, which uncovered no cytoplasmic effect, indicated that HSR can be attributed to additive-epistatic effects of three major gene pairs combined with those of polygenes. Major gene and polygene heritabilities were estimated to be 88.03% to 88.22% and 5.65% to 7.60%, respectively. Using the DH population, a genetic map was constructed with simple sequence repeat (SSR) markers anchored on nine linkage groups spanning 906.62 cM. Eight QTLs for HSR were located on chromosomes C4, C5, C7, and C9 based on 2 years of phenotypic data using both multiple-QTL mapping and inclusive composite interval mapping. The identified QTLs collectively explained 37.6% to 46.7% of phenotypic variation. Three or four major QTLs (Hsr 4.2, 7.2, 9.3, and/or 9.1) showing a relatively larger effect were robustly detected in different years or with different mapping methods. The HSR trait was shown to have a complex genetic basis. Results from QTL mapping and classical genetic analysis were consistent. Our results provide a foundation for further research on HSR genetic regulation and molecular marker-assisted selection (MAS) for HSR in cabbage.

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Regulation and Subfunctionalization of Flowering Time Genes in the Allotetraploid Oil Crop Brassica napus

Frontiers in Plant Science ◽

10.3389/fpls.2020.605155 ◽

2020 ◽

Vol 11 ◽

Author(s):

Sarah Schiessl

Keyword(s):

Brassica Napus ◽

Flowering Time ◽

Genetic Regulation ◽

Current Data ◽

Environmental Signals ◽

Oil Crop ◽

Current State ◽

Gene Copies ◽

Close Relationship ◽

Polyploid Crops

Flowering is a vulnerable, but crucial phase in building crop yield. Proper timing of this period is therefore decisive in obtaining optimal yields. However, genetic regulation of flowering integrates many different environmental signals and is therefore extremely complex. This complexity increases in polyploid crops which carry two or more chromosome sets, like wheat, potato or rapeseed. Here, I summarize the current state of knowledge about flowering time gene copies in rapeseed (Brassica napus), an important oil crop with a complex polyploid history and a close relationship to Arabidopsis thaliana. The current data show a high demand for more targeted studies on flowering time genes in crops rather than in models, allowing better breeding designs and a deeper understanding of evolutionary principles. Over evolutionary time, some copies of rapeseed flowering time genes changed or lost their original role, resulting in subfunctionalization of the respective homologs. For useful applications in breeding, such patterns of subfunctionalization need to be identified and better understood.

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SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Brassica napus

Plants ◽

10.3390/plants10112475 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2475

Author(s):

MMU Helal ◽

Rafaqat Ali Gill ◽

Minqiang Tang ◽

Li Yang ◽

Ming Hu ◽

...

Keyword(s):

Brassica Napus ◽

Flowering Time ◽

Genetic Architecture ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Oil Quality ◽

Snp Array ◽

Brassica Napus L ◽

Genome Wide ◽

Genomic Regions

Traits related to flowering time are the most promising agronomic traits that directly impact the seed yield and oil quality of rapeseed (Brassica napus L.). Developing early flowering and maturity rapeseed varieties is an important breeding objective in B. napus. Many studies have reported on days to flowering, but few have reported on budding, bolting, and the interval between bolting and DTF. Therefore, elucidating the genetic architecture of QTLs and genes regulating flowering time, we presented an integrated investigation on SNP and haplotype-based genome-wide association study of 373 diverse B. napus germplasm, which were genotyped by the 60K SNP array and were phenotyped in the four environments. The results showed that a total of 15 and 37 QTLs were detected from SNP and haplotype-based GWAS, respectively. Among them, seven QTL clusters were identified by haplotype-based GWAS. Moreover, three and eight environmentally stable QTLs were detected by SNP-GWAS and haplotype-based GWAS, respectively. By integrating the above two approaches and by co-localizing the four traits, ten (10) genomic regions were under selection on chromosomes A03, A07, A08, A10, C06, C07, and C08. Interestingly, the genomic regions FT.A07.1, FT.A08, FT.C06, and FT.C07 were identified as a novel. In these ten regions, a total of 197 genes controlling FT were detected, of which 14 highly expressed DEGs were orthologous to 13 Arabidopsis thaliana genes after integration with transcriptome results. In a nutshell, the above results uncovered the genetic architecture of important agronomic traits related to flowering time and provided a basis for multiple molecular marker-trait associations in B. napus.

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