Genetic analysis of morphological traits in a new, versatile, rapid-cycling Brassica rapa recombinant inbred line population

Cross-species transcriptomics reveals differential regulation of essential photosynthesis genes in Hirschfeldia incana

Photosynthesis is the only yield-related trait not yet substantially improved by plant breeding. Previously, we have established H. incana as the model plant for high photosynthetic light-use efficiency (LUE). Now we aim to unravel the genetic basis of this trait in H. incana, potentially contributing to the improvement of photosynthetic LUE in other species. Here, we compare its transcriptomic response to high light with that of Arabidopsis thaliana, Brassica rapa, and Brassica nigra, 3 fellow Brassicaceae members with lower photosynthetic LUE. We built a high-light, high-uniformity growing environment, in which the plants developed normally without signs of stress. We compared gene expression in contrasting light conditions across species, utilizing a panproteome to identify orthologous proteins. In-depth analysis of 3 key photosynthetic pathways showed a general trend of lower gene expression under high-light conditions for all 4 species. However, several photosynthesis-related genes in H. incana break this trend. We observed cases of constitutive higher expression (like antenna protein LHCB8), treatment-dependent differential expression (as for PSBE), and cumulative higher expression through simultaneous expression of multiple gene copies (like LHCA6). Thus, H. incana shows differential regulation of essential photosynthesis genes, with the light-harvesting complex as the first point of deviation. The effect of these expression differences on protein abundance and turnover, and ultimately the high photosynthetic LUE phenotype is relevant for further investigation. Furthermore, this transcriptomic resource of plants fully grown under, rather than briefly exposed to, a very high irradiance, will support the development of highly efficient photosynthesis in crops.

Novel quantitative trait loci from an interspecific Brassica rapa derivative improve pod shatter resistance in Brassica napus

Pod shatter is a trait of agricultural relevance that ensures plants dehisce seeds in their native environment and has been subjected to domestication and selection for non-shattering types in several broadacre crops. However, pod shattering causes a significant yield reduction in canola (Brassica napus L.) crops. An interspecific breeding line BC95042 derived from a B. rapa/B. napus cross showed improved pod shatter resistance (up to 12-fold than a shatter-prone B. napus variety). To uncover the genetic basis and improve pod shatter resistance in new varieties, we analysed F2 and F2:3 derived populations from the cross between BC95042 and an advanced breeding line, BC95041, and genotyped with 15,498 DArTseq markers. Through genome scan, interval and inclusive composite interval mapping analyses, we identified seven quantitative trait loci (QTLs) associated with pod rupture energy, a measure for pod shatter resistance or pod strength, and they locate on A02, A03, A05, A09 and C01 chromosomes. Both parental lines contributed alleles for pod shatter resistance. We identified five pairs of significant epistatic QTLs for additive x additive, additive dominance and dominance x dominance interactions between A01/C01, A03/A07, A07/C03, A03/C03, and C01/C02 chromosomes for rupture energy. QTL effects on A03/A07 and A01/C01 were in the repulsion phase. Comparative mapping identified several candidate genes (AG, ABI3, ARF3, BP1, CEL6, FIL, FUL, GA2OX2, IND, LATE, LEUNIG, MAGL15, RPL, QRT2, RGA, SPT and TCP10) underlying main QTL and epistatic QTL interactions for pod shatter resistance. Three QTLs detected on A02, A03, and A09 were near the FUL (FRUITFULL) homologues BnaA03g39820D and BnaA09g05500D. Focusing on the FUL, we investigated putative motifs, sequence variants and the evolutionary rate of its homologues in 373 resequenced B. napus accessions of interest. BnaA09g05500D is subjected to purifying selection as it had a low Ka/Ks ratio compared to other FUL homologues in B. napus. This study provides a valuable resource for genetic improvement for yield through an understanding of the genetic mechanism controlling pod shatter resistance in Brassica species.

The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency

Photosynthesis is a key process in sustaining plant and human life. Improving the photosynthetic capacity of agricultural crops is an attractive means to increase their yields. While the core mechanisms of photosynthesis are highly conserved in C₃ plants, these mechanisms are very flexible, allowing considerable diversity in photosynthetic properties. Among this diversity is the maintenance of high photosynthetic light-use efficiency at high irradiance as identified in a small number of exceptional C₃ species. Hirschfeldia incana, a member of the Brassicaceae family, is such an exceptional species, and because it is easy to grow, it is an excellent model for studying the genetic and physiological basis of this trait. Here, we present a reference genome of H. incana and confirm its high photosynthetic light-use efficiency. While H. incana has the highest photosynthetic rates found so far in the Brassicaceae, the light-saturated assimilation rates of closely related Brassica rapa and Brassica nigra are also high. The H. incana genome has extensively diversified from that of B. rapa and B. nigra through large chromosomal rearrangements, species-specific transposon activity, and differential retention of duplicated genes. Duplicated genes in H. incana, B. rapa, and B. nigra that are involved in photosynthesis and/or photoprotection show a positive correlation between copy number and gene expression, providing leads into the mechanisms underlying the high photosynthetic efficiency of these species. Our work demonstrates that the H. incana genome serves as a valuable resource for studying the evolution of high photosynthetic light-use efficiency and enhancing photosynthetic rates in crop species.

Revealing seed color variation and their possible association with yield and quality traits in a diversity panel of flax (Linum Usitatissimum L.)

Seed color is a vital quality determinant of flax, significant for consumers' acceptability, and determines the commercial values of seeds. Also, seed color as a phenotypic marker may be a convenient way to select the plants with desired traits. This study assessed a diversity panel representing 144 flax genotypes from diverse geographical origins for the existence of genetic variability for luminosity (L*) and chromaticity (a* and b*) seed color parameters, seed yield, and quality traits over two years. The genetic variance was significant for seed color parameters, demonstrating the presence of significant genetic variability, which provides a resource to objectively evaluate and select flax genotypes based on seed color according to the market demand. High heritability combined with the high genotypic coefficient of variation observed for seed yield, oil, and protein content suggested a better genetic gain upon selecting these traits. Seed yield, seed quality traits, and phenological traits showed significant negative correlation with L* and b* parameters and positive correlation with a* suggesting that the seeds' dark background and brown color can serve as marker characters to prescreen early-flowering, high-yielding and oil and protein-rich genotypes. Interestingly 48 brown-seeded genotypes were identified as early-flowering with short height, large seeds, high thousand seed weight, and capsule diameter. In addition, 34 genotypes were characterized by light-colored yellow seeds, large seeds, late-flowering with shorter height, and high branch numbers. Our results highlighted that North America and Australia-belonged genotypes were lighter yellow-seeded than the ones from other continents. Flax genotypes from South America and Asia were high-yielding, while genotypes from North America were low-yielding genotypes. Moreover, darker brown-seeded genotypes have prevailed in the South American continent.

Genetic analysis reveals three novel QTLs underpinning a butterfly egg-induced hypersensitive response-like cell death in Brassica rapa

BACKGROUND

Cabbage white butterflies (Pieris spp.) can be severe pests of Brassica crops such as Chinese cabbage, Pak choi (Brassica rapa) or cabbages (B. oleracea). Eggs of Pieris spp. can induce a hypersensitive response-like (HR-like) cell death which reduces egg survival in the wild black mustard (B. nigra). Unravelling the genetic basis of this egg-killing trait in Brassica crops could improve crop resistance to herbivory, reducing major crop losses and pesticides use. Here we investigated the genetic architecture of a HR-like cell death induced by P. brassicae eggs in B. rapa.

RESULTS

A germplasm screening of 56 B. rapa accessions, representing the genetic and geographical diversity of a B. rapa core collection, showed phenotypic variation for cell death. An image-based phenotyping protocol was developed to accurately measure size of HR-like cell death and was then used to identify two accessions that consistently showed weak (R-o-18) or strong cell death response (L58). Screening of 160 RILs derived from these two accessions resulted in three novel QTLs for Pieris brassicae-induced cell death on chromosomes A02 (Pbc1), A03 (Pbc2), and A06 (Pbc3). The three QTLs Pbc1-3 contain cell surface receptors, intracellular receptors and other genes involved in plant immunity processes, such as ROS accumulation and cell death formation. Synteny analysis with A. thaliana suggested that Pbc1 and Pbc2 are novel QTLs associated with this trait, while Pbc3 also contains an ortholog of LecRK-I.1, a gene of A. thaliana previously associated with cell death induced by a P. brassicae egg extract.

CONCLUSIONS

This study provides the first genomic regions associated with the Pieris egg-induced HR-like cell death in a Brassica crop species. It is a step closer towards unravelling the genetic basis of an egg-killing crop resistance trait, paving the way for breeders to further fine-map and validate candidate genes.

Advances and Challenges for QTL Analysis and GWAS in the Plant-Breeding of High-Yielding: A Focus on Rapeseed

Yield is one of the most important agronomic traits for the breeding of rapeseed (Brassica napus L), but its genetic dissection for the formation of high yield remains enigmatic, given the rapid population growth. In the present review, we review the discovery of major loci underlying important agronomic traits and the recent advancement in the selection of complex traits. Further, we discuss the benchmark summary of high-throughput techniques for the high-resolution genetic breeding of rapeseed. Biparental linkage analysis and association mapping have become powerful strategies to comprehend the genetic architecture of complex agronomic traits in crops. The generation of improved crop varieties, especially rapeseed, is greatly urged to enhance yield productivity. In this sense, the whole-genome sequencing of rapeseed has become achievable to clone and identify quantitative trait loci (QTLs). Moreover, the generation of high-throughput sequencing and genotyping techniques has significantly enhanced the precision of QTL mapping and genome-wide association study (GWAS) methodologies. Furthermore, this study demonstrates the first attempt to identify novel QTLs of yield-related traits, specifically focusing on ovule number per pod (ON). We also highlight the recent breakthrough concerning single-locus-GWAS (SL-GWAS) and multi-locus GWAS (ML-GWAS), which aim to enhance the potential and robust control of GWAS for improved complex traits.

Flowering Time Gene Variation in Brassica Species Shows Evolutionary Principles

Flowering time genes have a strong influence on successful reproduction and life cycle adaptation. However, their regulation is highly complex and only well understood in diploid model systems. For crops with a polyploid background from the genus Brassica, data on flowering time gene variation are scarce, although indispensable for modern breeding techniques like marker-assisted breeding. We have deep-sequenced all paralogs of 35 Arabidopsis thaliana flowering regulators using Sequence Capture followed by Illumina sequencing in two selected accessions of the vegetable species Brassica rapa and Brassica oleracea, respectively. Using these data, we were able to call SNPs, InDels and copy number variations (CNVs) for genes from the total flowering time network including central flowering regulators, but also genes from the vernalisation pathway, the photoperiod pathway, temperature regulation, the circadian clock and the downstream effectors. Comparing the results to a complementary data set from the allotetraploid species Brassica napus, we detected rearrangements in B. napus which probably occurred early after the allopolyploidisation event. Those data are both a valuable resource for flowering time research in those vegetable species, as well as a contribution to speciation genetics.

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

Crop plant architecture plays a highly important role in its agronomic performance. Plant height (PH) and primary branch number (PB) are two major factors that affect the plant architecture of rapeseed (Brassica napus). Previous studies have shown that these two traits are controlled by multiple quantitative trait loci (QTL); however, QTLs have not been delimited to regions less than 10cM. Genome-wide association study (GWAS) is a highly efficient approach for identifying genetic loci controlling traits at relatively high resolution. In this study, variations in PH and PB of a panel of 472 rapeseed accessions that had previously been analyzed by a 60k SNP array were investigated for three consecutive years and studied by GWAS. Eight QTLs on chromosome A03, A05, A07 and C07 were identified for PH, and five QTLs on A01, A03, A07 and C07 were identified for PB. Although most QTLs have been detected in previous studies based on linkage analyses, the two QTLs of PH on A05 and the QTL of PB on C07 were novel. In the genomic regions close to the GWAS peaks, orthologs of the genes involved in flower development, phytohormone biosynthesis, metabolism and signaling in Arabidopsis were identified.

A transposon insertion in FLOWERING LOCUS T is associated with delayed flowering in Brassica rapa

Long days and vernalization accelerate the transition from vegetative growth to reproductive growth in Brassica rapa. Bolting before plants reach the harvesting stage is a serious problem in B. rapa vegetable crop cultivation. The genetic dissection of flowering time is important for breeding of premature bolting-resistant B. rapa crops. Using a recombinant inbred line (RIL) population, we twice detected two major quantitative trait loci (QTLs) for flowering time in two different growing seasons that were located on chromosomes A02 and A07, respectively. We hypothesized that an orthologue of the Arabidopsis thaliana FLOWERING LOCUS T (FT) gene, named as BrFT2, was the candidate gene underlying the QTL localized to A07. A transposon insertion in the second intron of BrFT2 was detected in one of the parental lines, which was predicted to generate a loss-of-function allele. Transcription analysis revealed that the BrFT2 transcript was not present in the parental line that harbored the mutated allele. RILs carrying only the mutated BrFT2 allele showed delayed flowering regardless of growing seasons when compared to RILs carrying the wild-type BrFT2 allele. These data suggest that BrFT2 is involved in flowering time regulation in controlling flowering time in B. rapa.

Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Simple sequence repeats (SSRs) are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR) markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%), amplicons were successfully generated with high quality. Seventeen (89.5%) showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage.

RNAi-mediated down-regulation of SHATTERPROOF gene in transgenic oilseed rape

Oilseed rape is one of the important oil plants. Pod shattering is one of the problems in oilseed rape production especially in regions with dry conditions. One of the important genes in Brassica pod opening is SHATTERPROOF1 (SHP1). Down-regulation of BnSHP1 expression by RNAi can increase resistance to pod shattering. A 470 bp of the BnSHP1 cDNA sequence constructed in an RNAi-silencing vector was transferred to oilseed rape cv. SLM046. Molecular analysis of T2 transgenic plants by RT-PCR and Real-time PCR showed that expression of the BnSHP alleles was highly decreased in comparison with control plants. Morphologically, transgenic plants were normal and produced seeds at greenhouse conditions. At ripening, stage pods failed to shatter, and a finger pressure was needed for pod opening.

Recent progress in the use of 'omics technologies in brassicaceous vegetables

Continuing advances in 'omics methodologies and instrumentation is enhancing the understanding of how plants cope with the dynamic nature of their growing environment. 'Omics platforms have been only recently extended to cover horticultural crop species. Many of the most widely cultivated vegetable crops belong to the genus Brassica: these include plants grown for their root (turnip, rutabaga/swede), their swollen stem base (kohlrabi), their leaves (cabbage, kale, pak choi) and their inflorescence (cauliflower, broccoli). Characterization at the genome, transcript, protein and metabolite levels has illustrated the complexity of the cellular response to a whole series of environmental stresses, including nutrient deficiency, pathogen attack, heavy metal toxicity, cold acclimation, and excessive and sub-optimal irradiation. This review covers recent applications of 'omics technologies to the brassicaceous vegetables, and discusses future scenarios in achieving improvements in crop end-use quality.

Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato

A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.

Tetralocular ovary and high silique width in yellow sarson lines of Brassica rapa (subspecies trilocularis) are due to a mutation in Bra034340 gene, a homologue of CLAVATA3 in Arabidopsis

Genetic locus for tetralocular ovary (tet-o) in Brassica rapa was identified and it was shown that the number of locules and width of silique are associated. Brassica rapa is a highly polymorphic species containing many vegetables and oleiferous types. An interesting group of oleiferous types is the yellow sarson group (subspecies trilocularis) grown mostly in eastern India. This group contains lines that have bilocular ovaries, a defining trait of Brassicaceae, but also lines that have tetralocular ovaries. Yellow sarson lines commonly have high silique width which is further enhanced in the tetralocular types. We mapped the locus influencing tetralocular ovary in B. rapa using three mapping populations (F2, F6 and F7) derived from a cross between Chiifu (subspecies pekinensis, having bilocular ovary) and Tetralocular (having tetralocular ovary). QTL mapping of silique width was undertaken using the three mapping populations and a F2 population derived from a cross between Chiifu and YSPB-24 (a bilocular line belonging to yellow sarson group). Qualitative mapping of the trait governing locule number (tet-o) in B. rapa mapped the locus to linkage group A4. QTL mapping for silique width detected a major QTL on LG A4, co-mapping with the tet-o locus in bilocular/tetralocular cross. This QTL was not detected in the bilocular/bilocular cross. Saturation mapping of the tet-o region with SNP markers identified Bra034340, a homologue of CLAVATA3 of Arabidopsis thaliana, as the candidate gene for locule number. A C → T transition at position 176 of the coding sequence of Bra034340 revealed co-segregation with the tetralocular phenotype. The study of silique related traits is of interest both for understanding evolution under artificial selection and for breeding of cultivated Brassica species.

Genotype-environment interactions affecting preflowering physiological and morphological traits of Brassica rapa grown in two watering regimes

Plant growth and productivity are greatly affected by drought, which is likely to become more threatening with the predicted global temperature increase. Understanding the genetic architecture of complex quantitative traits and their interaction with water availability may lead to improved crop adaptation to a wide range of environments. Here, the genetic basis of 20 physiological and morphological traits is explored by describing plant performance and growth in a Brassica rapa recombinant inbred line (RIL) population grown on a sandy substrate supplemented with nutrient solution, under control and drought conditions. Altogether, 54 quantitative trait loci (QTL) were identified, of which many colocated in 11 QTL clusters. Seventeen QTL showed significant QTL-environment interaction (Q×E), indicating genetic variation for phenotypic plasticity. Of the measured traits, only hypocotyl length did not show significant genotype-environment interaction (G×E) in both environments in all experiments. Correlation analysis showed that, in the control environment, stomatal conductance was positively correlated with total leaf dry weight (DW) and aboveground DW, whereas in the drought environment, stomatal conductance showed a significant negative correlation with total leaf DW and aboveground DW. This correlation was explained by antagonistic fitness effects in the drought environment, controlled by a QTL cluster on chromosome A7. These results demonstrate that Q×E is an important component of the genetic variance and can play a great role in improving drought tolerance in future breeding programmes.

Genetic analysis of health-related secondary metabolites in a Brassica rapa recombinant inbred line population

The genetic basis of the wide variation for nutritional traits in Brassica rapa is largely unknown. A new Recombinant Inbred Line (RIL) population was profiled using High Performance Liquid Chromatography (HPLC) and Nuclear Magnetic Resonance (NMR) analysis to detect quantitative trait loci (QTLs) controlling seed tocopherol and seedling metabolite concentrations. RIL population parent L58 had a higher level of glucosinolates and phenylpropanoids, whereas levels of sucrose, glucose and glutamate were higher in the other RIL population parent, R-o-18. QTL related to seed tocopherol (α-, β-, γ-, δ-, α-/γ- and total tocopherol) concentrations were detected on chromosomes A3, A6, A9 and A10, explaining 11%–35% of the respective variation. The locus on A3 co-locates with the BrVTE1gene, encoding tocopherol cyclase. NMR spectroscopy identified the presence of organic/amino acid, sugar/glucosinolate and aromatic compounds in seedlings. QTL positions were obtained for most of the identified compounds. Compared to previous studies, novel loci were found for glucosinolate concentrations. This work can be used to design markers for marker-assisted selection of nutritional compounds in B. rapa.