Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus

Background

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation. Identification of large numbers of SNPs is helpful for genetic diversity analysis, map-based cloning, genome-wide association analyses and marker-assisted breeding. Recently, identifying genome-wide SNPs in allopolyploid Brassica napus (rapeseed, canola) by resequencing many accessions has become feasible, due to the availability of reference genomes of Brassica rapa (2n = AA) and Brassica oleracea (2n = CC), which are the progenitor species of B. napus (2n = AACC). Although many SNPs in B. napus have been released, the objective in the present study was to produce a larger, more informative set of SNPs for large-scale and efficient genotypic screening. Hence, short-read genome sequencing was conducted on ten elite B. napus accessions for SNP discovery. A subset of these SNPs was randomly selected for sequence validation and for genotyping efficiency testing using the Illumina GoldenGate assay.

Results

A total of 892,536 bi-allelic SNPs were discovered throughout the B. napus genome. A total of 36,458 putative amino acid variants were located in 13,552 protein-coding genes, which were predicted to have enriched binding and catalytic activity as a result. Using the GoldenGate genotyping platform, 94 of 96 SNPs sampled could effectively distinguish genotypes of 130 lines from two mapping populations, with an average call rate of 92%.

Conclusions

Despite the polyploid nature of B. napus, nearly 900,000 simple SNPs were identified by whole genome resequencing. These SNPs were predicted to be effective in high-throughput genotyping assays (51% polymorphic SNPs, 92% average call rate using the GoldenGate assay, leading to an estimated >450 000 useful SNPs). Hence, the development of a much larger genotyping array of informative SNPs is feasible. SNPs identified in this study to cause non-synonymous amino acid substitutions can also be utilized to directly identify causal genes in association studies.     

Genetic Variation for Life History Sensitivity to Seasonal Warming in Arabidopsis thaliana

Climate change has altered life history events in many plant species; however, little is known about genetic variation underlying seasonal thermal response. In this study, we simulated current and three future warming climates and measured flowering time across a globally diverse set of Arabidopsis thaliana accessions. We found that increased diurnal and seasonal temperature (1°–3°) decreased flowering time in two fall cohorts. The early fall cohort was unique in that both rapid cycling and overwintering life history strategies were revealed; the proportion of rapid cycling plants increased by 3–7% for each 1° temperature increase. We performed genome-wide association studies (GWAS) to identify the underlying genetic basis of thermal sensitivity. GWAS identified five main-effect quantitative trait loci (QTL) controlling flowering time and another five QTL with thermal sensitivity. Candidate genes include known flowering loci; a cochaperone that interacts with heat-shock protein 90; and a flowering hormone, gibberellic acid, a biosynthetic enzyme. The identified genetic architecture allowed accurate prediction of flowering phenotypes (R² > 0.95) that has application for genomic selection of adaptive genotypes for future environments. This work may serve as a reference for breeding and conservation genetic studies under changing environments.     

Genome Wide Analysis of Flowering Time Trait in Multiple Environments via High-Throughput Genotyping Technique in Brassica napus L.

The prediction of the flowering time (FT) trait in Brassica napus based on genome-wide markers and the detection of underlying genetic factors is important not only for oilseed producers around the world but also for the other crop industry in the rotation system in China. In previous studies the low density and mixture of biomarkers used obstructed genomic selection in B. napus and comprehensive mapping of FT related loci. In this study, a high-density genome-wide SNP set was genotyped from a double-haploid population of B. napus. We first performed genomic prediction of FT traits in B. napus using SNPs across the genome under ten environments of three geographic regions via eight existing genomic predictive models. The results showed that all the models achieved comparably high accuracies, verifying the feasibility of genomic prediction in B. napus. Next, we performed a large-scale mapping of FT related loci among three regions, and found 437 associated SNPs, some of which represented known FT genes, such as AP1 and PHYE. The genes tagged by the associated SNPs were enriched in biological processes involved in the formation of flowers. Epistasis analysis showed that significant interactions were found between detected loci, even among some known FT related genes. All the results showed that our large scale and high-density genotype data are of great practical and scientific values for B. napus. To our best knowledge, this is the first evaluation of genomic selection models in B. napus based on a high-density SNP dataset and large-scale mapping of FT loci.     

Genome-wide association study for flowering time,maturity dates and plant height in early maturing soybean (Glycine max) germplasm

Background

Soybean (Glycine max) is a photoperiod-sensitive and self-pollinated species. Days to flowering (DTF) and maturity (DTM), duration of flowering-to-maturity (DFTM) and plant height (PH) are crucial for soybean adaptability and yield. To dissect the genetic architecture of these agronomically important traits, a population consisting of 309 early maturity soybean germplasm accessions was genotyped with the Illumina Infinium SoySNP50K BeadChip and phenotyped in multiple environments. A genome-wide association study (GWAS) was conducted using a mixed linear model that involves both relative kinship and population structure.

Results

The linkage disequilibrium (LD) decayed slowly in soybean, and a substantial difference in LD pattern was observed between euchromatic and heterochromatic regions. A total of 27, 6, 18 and 27 loci for DTF, DTM, DFTM and PH were detected via GWAS, respectively. The Dt1 gene was identified in the locus strongly associated with both DTM and PH. Ten candidate genes homologous to Arabidopsis flowering genes were identified near the peak single nucleotide polymorphisms (SNPs) associated with DTF. Four of them encode MADS-domain containing proteins. Additionally, a pectin lyase-like gene was also identified in a major-effect locus for PH where LD decayed rapidly.

Conclusions

This study identified multiple new loci and refined chromosomal regions of known loci associated with DTF, DTM, DFTM and/or PH in soybean. It demonstrates that GWAS is powerful in dissecting complex traits and identifying candidate genes although LD decayed slowly in soybean. The loci and trait-associated SNPs identified in this study can be used for soybean genetic improvement, especially the major-effect loci associated with PH could be used to improve soybean yield potential. The candidate genes may serve as promising targets for studies of molecular mechanisms underlying the related traits in soybean.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1441-4) contains supplementary material, which is available to authorized users.     

Quantitative trait loci for seed yield and yield-related traits, and their responses to reduced phosphorus supply in Brassica napus

Background and Aims

One of the key targets of breeding programmes in rapeseed (Brassica napus) is to develop high-yield varieties. However, the lack of available phosphorus (P) in soils seriously limits rapeseed production. The aim of this study was to dissect the genetic control of seed yield and yield-related traits in B. napus grown with contrasting P supplies.

Methods

Two-year field trials were conducted at one site with normal and low P treatments using a population of 124 recombinant inbred lines derived from a cross between ‘B104-2’ and ‘Eyou Changjia’. Seed yield, seed weight, seed number, pod number, plant height, branch number and P efficiency coefficient (PEC) were investigated. Quantitative trait locus (QTL) analysis was performed by composite interval mapping.

Key Results

The phenotypic values of most of the tested traits were reduced under the low P conditions. In total, 74 putative QTLs were identified, contributing 7·3–25·4 % of the phenotypic variation. Of these QTLs, 16 (21·6 %) were detected in two seasons and in the mean value of two seasons, and eight QTLs for two traits were conserved across P levels. Low-P-specific QTLs were clustered on chromosomes A1, A6 and A8. By comparative mapping between Arabidopsis and B. napus, 161 orthologues of 146 genes involved in Arabidopsis P homeostasis and/or yield-related trait control were associated with 45 QTLs corresponding to 23 chromosomal regions. Four gene-based markers developed from genes involved in Arabidopsis P homeostasis were mapped to QTL intervals.

Conclusions

Different genetic determinants were involved in controlling seed yield and yield-related traits in B. napus under normal and low P conditions. The QTLs detected under reduced P supply may provide useful information for improving the seed yield of B. napus in soils with low P availability in marker-assisted selection.     

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

Background and AimsOilseed rape (Brassica napus) is one of the most important oil crops worldwide. Phosphorus (P) deficiency severely decreases the plant height and branch number of B. napus. However, the genetic bases controlling plant height and branch number in B. napus under P deficiency remain largely unknown. This study aims to mine candidate genes for plant height and branch number by genome-wide association study (GWAS) and determine low-P-tolerance haplotypes.MethodsAn association panel of B. napus was grown in the field with a low P supply (P, 0 kg ha⁻¹) and a sufficient P supply (P, 40 kg ha⁻¹) across 2 years and plant height and branch number were investigated. More than five million single-nucleotide polymorphisms (SNPs) were used to conduct GWAS of plant height and branch number at two contrasting P supplies.Key ResultsA total of 2127 SNPs were strongly associated (P < 6·25 × 10⁻⁰⁷) with plant height and branch number at two P supplies. There was significant correlation between phenotypic variation and the number of favourable 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 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 greater plant height than lines carrying other haplotype alleles at low P supply.ConclusionOur results demonstrate the power of GWAS in identifying genes of interest in B. napus and provided insights into the genetic basis of plant height and branch number at low P supply in B. napus. Candidate genes and favourable haplotypes may facilitate marker-based breeding efforts aimed at improving P use efficiency in B. napus.     

Quantitative Trait Loci for Thermal Time to Flowering and Photoperiod Responsiveness Discovered in Summer Annual-Type Brassica napus L

Time of flowering is a key adaptive trait in plants and is conditioned by the interaction of genes and environmental cues including length of photoperiod, ambient temperature and vernalisation. Here we investigated the photoperiod responsiveness of summer annual-types of Brassica napus (rapeseed, canola). A population of 131 doubled haploid lines derived from a cross between European and Australian parents was evaluated for days to flowering, thermal time to flowering (measured in degree-days) and the number of leaf nodes at flowering in a compact and efficient glasshouse-based experiment with replicated short and long day treatments. All three traits were under strong genetic control with heritability estimates ranging from 0.85–0.93. There was a very strong photoperiod effect with flowering in the population accelerated by 765 degree-days in the long day versus short day treatments. However, there was a strong genetic correlation of line effects (0.91) between the long and short day treatments and relatively low genotype x treatment interaction indicating that photoperiod had a similar effect across the population. Bivariate analysis of thermal time to flowering in short and long days revealed three main effect quantitative trait loci (QTLs) that accounted for 57.7% of the variation in the population and no significant interaction QTLs. These results provided insight into the contrasting adaptations of Australian and European varieties. Both parents responded to photoperiod and their alleles shifted the population to earlier flowering under long days. In addition, segregation of QTLs in the population caused wide transgressive segregation in thermal time to flowering. Potential candidate flowering time homologues located near QTLs were identified with the aid of the Brassica rapa reference genome sequence. We discuss how these results will help to guide the breeding of summer annual types of B. napus adapted to new and changing environments.     

Genome-Wide Analysis of Seed Acid Detergent Lignin (ADL) and Hull Content in Rapeseed (Brassica napus L.)

A stable yellow-seeded variety is the breeding goal for obtaining the ideal rapeseed (Brassica napus L.) plant, and the amount of acid detergent lignin (ADL) in the seeds and the hull content (HC) are often used as yellow-seeded rapeseed screening indices. In this study, a genome-wide association analysis of 520 accessions was performed using the Q + K model with a total of 31,839 single-nucleotide polymorphism (SNP) sites. As a result, three significant associations on the B. napus chromosomes A05, A09, and C05 were detected for seed ADL content. The peak SNPs were within 9.27, 14.22, and 20.86 kb of the key genes BnaA.PAL4, BnaA.CAD2/BnaA.CAD3, and BnaC.CCR1, respectively. Further analyses were performed on the major locus of A05, which was also detected in the seed HC examination. A comparison of our genome-wide association study (GWAS) results and previous linkage mappings revealed a common chromosomal region on A09, which indicates that GWAS can be used as a powerful complementary strategy for dissecting complex traits in B. napus. Genomic selection (GS) utilizing the significant SNP markers based on the GWAS results exhibited increased predictive ability, indicating that the predictive ability of a given model can be substantially improved by using GWAS and GS.     

In silico integration of quantitative trait loci for seed yield and yield-related traits in Brassica napus

Mapping quantitative trait loci (QTLs) is a foundation for molecular marker-assisted selection and map-based gene cloning. During the past decade, numerous QTLs for seed yield (SY) and yield-related traits in Brassica napus L. have been identified. However, integration of these results in order to compare QTLs from different mapping populations has not been undertaken, due to the lack of common molecular markers between studies. Using previously reported Brassica rapa and Brassica oleracea genome sequences, we carried out in silico integration of 1,960 QTLs associated with 13 SY and yield-related traits from 15 B. napus mapping experiments over the last decade. A total of 736 SY and yield-related QTLs were mapped onto 283 loci in the A and C genomes of B. napus. These QTLs were unevenly distributed across the 19 B. napus chromosomes, with the most on chromosome A3 and the least on chromosome C6. Our integrated QTL map identified 142 loci where the conserved QTLs were detected and 25 multifunctional loci, mostly for the traits of flowering time (FT), plant height, 1,000-seed weight, maturity time and SY. These conserved QTLs and multifunctional loci may result from pleiotropism or clustered genes. At the same time, a total of 146 genes underlying the QTLs for FT and other yield-related traits were identified by comparative mapping with the Arabidopsis genome. These results facilitate the retrieval of B. napus SY and yield-related QTLs for research communities, increase the density of targeted QTL-linked markers, validate the existence of QTLs across different populations, and advance the fine mapping of genes.     

Genetic and physical mapping of flowering time loci in canola (Brassica napus L.)

We identified quantitative trait loci (QTL) underlying variation for flowering time in a doubled haploid (DH) population of vernalisation—responsive canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum and aligned them with physical map positions of predicted flowering genes from the Brassica rapa genome. Significant genetic variation in flowering time and response to vernalisation were observed among the DH lines from Skipton/Ag-Spectrum. A molecular linkage map was generated comprising 674 simple sequence repeat, sequence-related amplified polymorphism, sequence characterised amplified region, Diversity Array Technology, and candidate gene based markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 20 loci, localised on ten different chromosomes. These loci each accounted for between 2.4 and 28.6 % of the total genotypic variation for first flowering and response to vernalisation. However, identification of consistent QTL was found to be dependant upon growing environments. We compared the locations of QTL with the physical positions of predicted flowering time genes located on the sequenced genome of B. rapa. Some QTL associated with flowering time on A02, A03, A07, and C06 may represent homologues of known flowering time genes in Arabidopsis; VERNALISATION INSENSITIVE 3, APETALA1, CAULIFLOWER, FLOWERING LOCUS C, FLOWERING LOCUS T, CURLY LEAF, SHORT VEGETATIVE PHASE, GA3 OXIDASE, and LEAFY. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for low rainfall areas, via marker-assisted selection.     

Comparative mapping of loci controlling winter survival and related traits in oilseed Brassica rapa and B. napus

Winter survival is an important characteristic of oilseedBrassica that is seeded in the fall in northern climates,and it may be affected by genetic variation for other cold-regulated traits,such as freezing tolerance and vernalization responsive flowering time. Weanalyzed immortalized populations of oilseed Brassica rapa(recombinant inbred lines) and B. napus (double haploidlines) derived from crosses of annual and biennial types in order to comparethe map positions and effects of quantitative trait loci controlling wintersurvival, nonacclimated and acclimated freezing tolerances, and flowering time.The B. napus population was evaluated in multiple winters,and six of the 16 total significant QTL for winter survival were detected inmore than one winter. Correspondence in the map positions of QTL controllingdifferent traits within species provided evidence that some alleles causinggreater acclimated freezing tolerance and later flowering time also contributedto increased winter survival. Correspondence in the map positions of QTLbetween species provided evidence for allelic variation at homologous loci inB. rapa and B. napus. The potentialrole of some candidate genes in regulating these traits is discussed.     

Whole‐transcriptome analysis reveals genetic factors underlying flowering time regulation in rapeseed (Brassica napus L.)

Rapeseed (Brassica napus L.), one of the most important sources of vegetable oil and protein‐rich meals worldwide, is adapted to different geographical regions by modification of flowering time. Rapeseed cultivars have different day length and vernalization requirements, which categorize them into winter, spring, and semiwinter ecotypes. To gain a deeper insight into genetic factors controlling floral transition in B. napus, we performed RNA sequencing (RNA‐seq) in the semiwinter doubled haploid line, Ningyou7, at different developmental stages and temperature regimes. The expression profiles of more than 54,000 gene models were compared between different treatments and developmental stages, and the differentially expressed genes were considered as targets for association analysis and genetic mapping to confirm their role in floral transition. Consequently, 36 genes with association to flowering time, seed yield, or both were identified. We found novel indications for neofunctionalization in homologs of known flowering time regulators like VIN3 and FUL. Our study proved the potential of RNA‐seq along with association analysis and genetic mapping to identify candidate genes for floral transition in rapeseed. The candidate genes identified in this study could be subjected to genetic modification or targeted mutagenesis and genotype building to breed rapeseed adapted to certain environments.     

Analysis of genetic factors that control shoot mineral concentrations in rapeseed (Brassica napus) in different boron environments

Mineral nutrients are essential for plant cell function, and understanding the genetic and physiological basis of mineral concentration is therefore important for the development of nutrient-efficient crop varieties that can cope with a shortage of mineral resources. In the present study, we investigated the profiles of B, Ca, Fe, Cu, Mg, P and Zn concentrations in shoots and analyzed the genetic variation in a rapeseed (Brassica napus) double haploid population at normal and deficient boron (B) levels in hydroponic conditions. Significant correlations between the concentrations of different minerals, such as Ca and Mg, Ca and P, and Cu and Fe, existed in both B environments. A total of 35 quantitative trait loci (QTL) and 74 epistatic interaction pairs for mineral concentrations were identified by whole genome analysis of QTL and epistatic interactions. The individual phenotypic contributions of the QTL ranged from 4.4% to 19.0%, and the total percentage of genetic variance that was due to QTL and epistatic interactions varied from 10.4% to 82.4%. Most of these QTL corresponded specifically to one of the two B conditions except for one stable main-effect P-QTL across the B environments. Three QTL for Ca and Mg were found to co-localize under normal B condition. These results revealed that genetic factors control mineral homeostasis in plants and multigenes involving ion transport are required to regulate mineral balance in plants under conditions of diverse nutrient stress. In addition, 26 genes involved in ion uptake and transport in Arabidopsis thaliana were in silico mapped onto the QTL intervals of B. napus by comparative genomic analysis. These candidate orthologous genes in B. napus allowed the selection of genes involved in the controlling mineral concentration that may account for the identified QTL.     

Mapping of days to flower and seed yield in spring oilseed <Emphasis Type="Italic">Brassica napus</Emphasis> carrying genome content introgressed from <Emphasis Type="Italic">Brassica oleracea</Emphasis>

Earliness of flowering and maturity and high seed yield are important objectives of breeding spring Brassica napus canola. Previously, we have introgressed earliness of flowering from Brassica oleracea into spring B. napus canola through interspecific crossing between these two species. In this paper, we report quantitative trait locus (QTL) mapping of days to flower and seed yield by use of publicly available markers and markers designed based on flowering time genes and a doubled haploid population, derived from crossing of the spring canola parent and an early flowering line developed from a B. napus × B. oleracea cross, tested in nine field trials for over 5 years. Five genomic regions associated with days to flower were identified on C1, C2, C3, and C6 of which the single QTL of C1 was detected in all trials; in all cases, the allele introgressed from B. oleracea reduced the number of days to flower. BLASTn search in the Brassica genomes located the physical position of the QTL markers and identified putative flowering time genes in these regions. In the case of seed yield, ten QTL from eight linkage groups were detected; however, none could be consistently detected in all trials. The QTL region of C1 associated with days to flower did not show significant association with seed yield in more than 80% of the field trials; however, in a single trial, the allele introgressed from B. oleracea exerted a negative effect on seed yield. Thus, the genomic regions and molecular markers identified in this research could potentially be used in breeding for the development of early flowering B. napus canola cultivars without affecting seed yield in a majority of the environments.     

A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus

Background

Single nucleotide polymorphism (SNP) markers have a wide range of applications in crop genetics and genomics. Due to their polyploidy nature, many important crops, such as wheat, cotton and rapeseed contain a large amount of repeat and homoeologous sequences in their genomes, which imposes a huge challenge in high-throughput genotyping with sequencing and/or array technologies. Allotetraploid Brassica napus (AACC, 2n = 4x = 38) comprises of two highly homoeologous sub-genomes derived from its progenitor species B. rapa (AA, 2n = 2x = 20) and B. oleracea (CC, 2n = 2x = 18), and is an ideal species to exploit methods for reducing the interference of extensive inter-homoeologue polymorphisms (mHemi-SNPs and Pseudo-simple SNPs) between closely related sub-genomes.

Results

Based on a recent B. napus 6K SNP array, we developed a bi-filtering procedure to identify unauthentic lines in a DH population, and mHemi-SNPs and Pseudo-simple SNPs in an array data matrix. The procedure utilized both monomorphic and polymorphic SNPs in the DH population and could effectively distinguish the mHemi-SNPs and Pseudo-simple SNPs that resulted from superposition of the signals from multiple SNPs. Compared with conventional procedure for array data processing, the bi-filtering method could minimize the pseudo linkage relationship caused by the mHemi-SNPs and Pseudo-simple SNPs, thus improving the quality of SNP genetic map. Furthermore, the improved genetic map could increase the accuracies of mapping of QTLs as demonstrated by the ability to eliminate non-real QTLs in the mapping population.

Conclusions

The bi-filtering analysis of the SNP array data represents a novel approach to effectively assigning the multi-loci SNP genotypes in polyploid B. napus and may find wide applications to SNP analyses in polyploid crops.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1559-4) contains supplementary material, which is available to authorized users.     

Intergenomic single nucleotide polymorphisms as a tool for bacterial artificial chromosome contig building of homoeologous Brassica napus regions

Background

Homoeologous sequences pose a particular challenge if bacterial artificial chromosome (BAC) contigs shall be established for specific regions of an allopolyploid genome. Single nucleotide polymorphisms (SNPs) differentiating between homoeologous genomes (intergenomic SNPs) may represent a suitable screening tool for such purposes, since they do not only identify homoeologous sequences but also differentiate between them.

Results

Sequence alignments between Brassica rapa (AA) and Brassica oleracea (CC) sequences mapping to corresponding regions on chromosomes A1 and C1, respectively were used to identify single nucleotide polymorphisms between the A and C genomes. A large fraction of these polymorphisms was also present in Brassica napus (AACC), an allopolyploid species that originated from hybridisation of A and C genome species. Intergenomic SNPs mapping throughout homoeologous chromosome segments spanning approximately one Mbp each were included in Illumina’s GoldenGate® Genotyping Assay and used to screen multidimensional pools of a Brassica napus bacterial artificial chromosome library with tenfold genome coverage. Based on the results of 50 SNP assays, a BAC contig for the Brassica napus A subgenome was established that spanned the entire region of interest. The C subgenome region was represented in three BAC contigs.

Conclusions

This proof-of-concept study shows that sequence resources of diploid progenitor genomes can be used to deduce intergenomic SNPs suitable for multiplex polymerase chain reaction (PCR)-based screening of multidimensional BAC pools of a polyploid organism. Owing to their high abundance and ease of identification, intergenomic SNPs represent a versatile tool to establish BAC contigs for homoeologous regions of a polyploid genome.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-560) contains supplementary material, which is available to authorized users.     

Overexpression of a Brassica rapa MADS-box gene, BrAGL20, induces early flowering time phenotypes in Brassica napus

BrAGL20 (SOC1) containing MADS box, a floral integrator gene, was introduced into Brassica napus cv. “Youngsan” by Agrobacterium-mediated transformation. Constitutively overexpressed BrAGL20 under the CaMV 35S promoter induced early flowering time compared to the wild-type. These phenotypes were stably inherited through generations T₂ and T₃, regardless of planting season. The expression of the floral meristem identity genes LFY and AP1 seemed to appear rapidly in the shoot apex region of transgenic plants showing the early flowering time phenotype. These results suggest that overexpression of BrAGL20 can significantly affect the flowering time of B. napus, and regulation of floral integrator gene expression could be applied for adaptation of crops to local environments and climate changes.     

A High-Density Genetic Map Identifies a Novel Major QTL for Boron Efficiency in Oilseed Rape (Brassica napus L.)

Low boron (B) seriously limits the growth of oilseed rape (Brassica napus L.), a high B demand species that is sensitive to low B conditions. Significant genotypic variations in response to B deficiency have been observed among B. napus cultivars. To reveal the genetic basis for B efficiency in B. napus, quantitative trait loci (QTLs) for the plant growth traits, B uptake traits and the B efficiency coefficient (BEC) were analyzed using a doubled haploid (DH) population derived from a cross between a B-efficient parent, Qingyou 10, and a B-inefficient parent, Westar 10. A high-density genetic map was constructed based on single nucleotide polymorphisms (SNPs) assayed using Brassica 60 K Infinium BeadChip Array, simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs). The linkage map covered a total length of 2139.5 cM, with 19 linkage groups (LGs) and an average distance of 1.6 cM between adjacent markers. Based on hydroponic evaluation of six B efficiency traits measured in three separate repeated trials, a total of 52 QTLs were identified, accounting for 6.14–46.27% of the phenotypic variation. A major QTL for BEC, qBEC-A3a, was co-located on A3 with other QTLs for plant growth and B uptake traits under low B stress. Using a subset of substitution lines, qBEC-A3a was validated and narrowed down to the interval between CNU384 and BnGMS436. The results of this study provide a novel major locus located on A3 for B efficiency in B. napus that will be suitable for fine mapping and marker-assisted selection breeding for B efficiency in B. napus.