Genetic architecture and mechanism of seed number per pod in rapeseed: elucidated through linkage and near-isogenic line analysis

Systematic trait dissection in oilseed rape provides a comprehensive view, further insight, and exact roadmap for yield determination

Background

Yield is the most important and complex trait that is influenced by numerous relevant traits with very complicated interrelations. While there are a large number of studies on the phenotypic relationship and genetic basis of yield traits, systematic studies with further dissection focusing on yield are limited. Therefore, there is still lack of a comprehensive and in-depth understanding of the determination of yield.

Results

In this study, yield was systematically dissected at the phenotypic, genetic to molecular levels in oilseed rape (Brassica napus L.). The analysis of correlation, network, and principal component for 21 traits in BnaZN-RIL population showed that yield was determined by a complex trait network with key contributors. The analysis of the constructed high-density single nucleotide polymorphism (SNP) linkage map revealed the concentrated distribution of distorted and heterozygous markers, likely due to selection on genes controlling the growth period and yield heterosis. A total of 134 consensus quantitative trait loci (QTL) were identified for 21 traits, of which all were incorporated into an interconnecting QTL network with dozens of hub-QTL. Four representative hub-QTL were further dissected to the target or candidate genes that governed the causal relationships between the relevant traits.

Conclusions

The highly consistent results at the phenotypic, genetic, and molecular dissecting demonstrated that yield was determined by a multilayer composite network that involved numerous traits and genes showing complex up/down-stream and positive/negative regulation. This provides a systematic view, further insight, and exact roadmap for yield determination, which represents a significant advance toward the understanding and dissection of complex traits.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02134-w.

Genome-wide characterization of ovate family protein gene family associated with number of seeds per silique in Brassica napus

Ovate family proteins (OFPs) were firstly identified in tomato as proteins controlling the pear shape of the fruit. Subsequent studies have successively proved that OFPs are a class of negative regulators of plant development, and are involved in the regulation of complex traits in different plants. However, there has been no report about the functions of OFPs in rapeseed growth to date. Here, we identified the OFPs in rapeseed at the genomic level. As a result, a total of 67 members were obtained. We then analyzed the evolution from Arabidopsis thaliana to Brassica napus, illustrated their phylogenetic and syntenic relationships, and compared the gene structure and conserved domains between different copies. We also analyzed their expression patterns in rapeseed, and found significant differences in the expression of different members and in different tissues. Additionally, we performed a GWAS for the number of seeds per silique (NSPS) in a rapeseed population consisting of 204 natural accessions, and identified a new gene BnOFP13_2 significantly associated with NSPS, which was identified as a novel function of OFPs. Haplotype analysis revealed that the accessions with haplotype 3 had a higher NSPS than other accessions, suggesting that BnOFP13_2 is associated with NSPS. Transcript profiling during the five stages of silique development demonstrated that BnOFP13_2 negatively regulates NSPS. These findings provide evidence for functional diversity of OFP gene family and important implications for oilseed rape breeding.

Gamma Rays and Sodium Azide Induced Genetic Variability in High-Yielding and Biofortified Mutant Lines in Cowpea [Vigna unguiculata (L.) Walp.]

With the twin pressures of high population growth and extreme weather events, developing countries are the worst hit in meeting the food demands of their people, with millions unable to access adequate and nutritionally balanced food. Crop production must be increased by 70% to keep up with the food demands of a rapidly growing population, which is expected to rise to 9.6 billion by 2050. Legumes are ideal food crops to increase agricultural productivity and achieve sustainable development goals. Cowpea, a warm-season grain legume, is often categorized as a neglected crop with immense scope for genetic improvement through proper breeding strategies. A multi-year field experiment of induced mutagenesis was conducted to increase seed yield and genetic variability in the agro-economic traits of two cowpea varieties treated with different doses of gamma (γ) rays and sodium azide (SA). The study was also aimed to optimize different doses of γ rays and SA employed individually and in combinations. Quantitative trait analysis revealed a maximum increase in seed yield from M₂ to M₃ generation. Among the 10 quantitative traits studied, seeds per pod and seed weight positively correlated with a major direct impact on yield. An extensive phenotypic selection cycle from M₂-M₄ generations resulted in isolating new high-yielding and nutrient-dense mutant lines. Such high-yielding biofortified mutant lines with enhanced genetic variability could serve as a donor of elite genes and represent a valuable genetic resource for improving low-yielding warm-season grain legumes.

A Preliminary Study for Identifying Quantitative Trait Loci Associated with Seed Production in Radish Using Genotyping-by-Sequencing

The high yield of seeds can reduce the cost of seed production for parental lines, as well as F1 cultivars in radish. The number of seeds per silique and silique length are two important traits among traits determining seed yield, but no study has been conducted on their quantitative trait loci (QTLs) in radish. A high-density linkage map was constructed, based on genotyping-by-sequencing (GBS) of the F2 population, derived from two parental lines, significantly differed by the two traits, which were grown in a controlled environment to minimize the environmental effects. Using the map with 848 SNPs, three significant QTLs were identified, two and one of which were associated with the number of seeds per silique and silique length, respectively. Ortholog analysis was conducted with Arabidopsis thaliana genes, related to the number of seeds per silique, and revealed five radish putative candidate genes. These putative candidate genes appear to be related to ovule, embryo sac, embryo, pollen and seed development, as well as a double fertilization process. The method to pollinate the F2 population, as well as preliminary QTLs and SNPs therein, can be helpful for future QTL studies to improve seed production in radish breeding programs.

Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus

Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.

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

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.

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.

Uncovering Trait Associations Resulting in Maximal Seed Yield in Winter and Spring Oilseed Rape

Seed yield is a complex trait for many crop species including oilseed rape (OSR) (Brassica napus), the second most important oilseed crop worldwide. Studies have focused on the contribution of distinct factors in seed yield such as environmental cues, agronomical practices, growth conditions, or specific phenotypic traits at the whole plant level, such as number of pods in a plant. However, how female reproductive traits contribute to whole plant level traits, and hence to seed yield, has been largely ignored. Here, we describe the combined contribution of 33 phenotypic traits within a B. napus diversity set population and their trade-offs at the whole plant and organ level, along with their interaction with plant level traits. Our results revealed that both Winter OSR (WOSR) and Spring OSR (SOSR); the two more economically important OSR groups in terms of oil production; share a common dominant reproductive strategy for seed yield. In this strategy, the main inflorescence is the principal source of seed yield, producing a good number of ovules, a large number of long pods with a concomitantly high number of seeds per pod. Moreover, we observed that WOSR opted for additional reproductive strategies than SOSR, presenting more plasticity to maximise seed yield. Overall, we conclude that OSR adopts a key strategy to ensure maximal seed yield and propose an ideal ideotype highlighting crucial phenotypic traits that could be potential targets for breeding.

Fine mapping and candidate gene analysis of a major locus controlling ovule abortion and seed number per silique in Brassica napus L

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. 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 explore 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 associates with multiple 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 ovules (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 an 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.

Both overlapping and independent loci underlie seed number per pod and seed weight in Brassica napus by comparative quantitative trait loci analysis

Seed number per pod (SNPP) and seed weight (SW) are two components of seed yield in rapeseed (Brassica napus). Here, a natural population of rapeseed was employed for genome-wide association analysis for SNPP and SW across multi-years. A total of 101 and 77 SNPs significantly associated with SNPP and SW with the phenotypic variances (R2) ranging from 1.35 to 29.47% and from 0.78 to 34.58%, respectively. And 43 and 33 homologs of known genes from model plants were located in the 65 and 49 haplotype blocks (HBs) for SNPP and SW, respectively. Notably, we found 5 overlapping loci and 3 sets of loci with collinearity for both SNPP and SW, of which 4 overlapping loci harbored the haplotypes with the same direction of genetic effects on SNPP and SW, indicating high possibility to simultaneously improve SNPP and SW in rapeseed. Our findings revealed both overlapping and independent loci controlling seed number per pod and seed weight in rapeseed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01232-1.

An evolutionary population structure model reveals pleiotropic effects of GmPDAT for traits related to seed size and oil content in soybean

Seed oil traits in soybean that are of benefit to human nutrition and health have been selected for during crop domestication. However, these domesticated traits have significant differences across various evolutionary types. In this study, we found that the integration of evolutionary population structure (evolutionary types) with genome-wide association studies increased the power of gene detection, and it identified one locus for traits related to seed size and oil content on chromosome 13. This domestication locus, together with another one in a 200-kb region, was confirmed by the GEMMA and EMMAX software. The candidate gene, GmPDAT, had higher expressional levels in high-oil and large-seed accessions than in low-oil and small-seed accessions. Overexpression lines had increased seed size and oil content, whereas RNAi lines had decreased seed size and oil content. The molecular mechanism of GmPDAT was deduced based on results from linkage analysis for triacylglycerols and on histocytological comparisons of transgenic soybean seeds. Our results illustrate a new approach for identifying domestication genes with pleiotropic effects.

High-throughput phenotyping accelerates the dissection of the dynamic genetic architecture of plant growth and yield improvement in rapeseed

Rapeseed is the second most important oil crop species and is widely cultivated worldwide. However, overcoming the 'phenotyping bottleneck' has remained a significant challenge. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In addition, it is important to explore the dynamic genetic architecture underlying rapeseed plant growth and its contribution to final yield. In this work, a high-throughput phenotyping facility was used to dynamically screen a rapeseed intervarietal substitution line population during two growing seasons. We developed an automatic image analysis pipeline to quantify 43 dynamic traits across multiple developmental stages, with 12 time points. The time-resolved i-traits could be extracted to reflect shoot growth and predict the final yield of rapeseed. Broad phenotypic variation and high heritability were observed for these i-traits across all developmental stages. A total of 337 and 599 QTLs were identified, with 33.5% and 36.1% consistent QTLs for each trait across all 12 time points in the two growing seasons, respectively. Moreover, the QTLs responsible for yield indicators colocalized with those of final yield, potentially providing a new mechanism of yield regulation. Our results indicate that high-throughput phenotyping can provide novel insights into the dynamic genetic architecture of rapeseed growth and final yield, which would be useful for future genetic improvements in rapeseed.

QTL Mapping for Domestication-Related Characteristics in Field Cress (Lepidium campestre)-A Novel Oil Crop for the Subarctic Region

Domestication of a new crop requires identification and improvement of desirable characteristics Field cress (Lepidium campestre) is being domesticated as a new oilseed crop, particularly for northern temperate regions.. In the present study, an F₂ mapping population and its F₃ progenies were used to identify quantitative trait loci (QTLs) for plant height (PH), number of stems per plant (NS), stem growth orientation (SO), flowering habit (FH), earliness (ER), seed yield per plant (SY), pod shattering resistance (SHR), and perenniality (PE). A highly significant correlation (p < 0.001) was observed between several pairs of characteristics, including SY and ER (negative) or ER and PE (positive). The inclusive composite interval mapping approach was used for QTL mapping using 2330 single nucleotide polymorphism (SNP) markers mapped across the eight field cress linkage groups. Nine QTLs were identified with NS, PH, SO, and PE having 3, 3, 2, and 1 QTLs, explaining 21.3%, 29.5%, 3.8%, and 7.2% of the phenotypic variation, respectively. Candidate genes behind three of the QTLs and favorable marker alleles for different classes of each characteristic were identified. Following their validation through further study, the identified QTLs and associated favorable marker alleles can be used in marker-aided breeding to speed up the domestication of field cress.

Validation and Characterization of a Seed Number Per Silique Quantitative Trait Locus qSN.A7 in Rapeseed (Brassica napus L.)

Seed number is a key character/trait tightly related to the plant fitness/evolution and crop domestication/improvement. The seed number per silique (SNPS) shows a huge variation from several to more than 30, however the underlying regulatory mechanisms are poorly known, which has hindered its improvement. To answer this question, several representative lines with extreme SNPS were previously subjected to systematic genetic and cytological analyses. The results showed that the natural variation of seed number per silique is mainly controlled by maternal and embryonic genotype, which are co-determined by ovule number per ovary, fertile ovule ratio, ovule fertilization rate, and fertilized ovule development rate. More importantly, we also mapped two repeatable quantitative trait loci (QTLs) for SNPS using the F2:3 population derived from Zhongshuang11 and No. 73290, of which the major QTL qSN.A6 has been fine-mapped. In the current study, the near-isogenic lines (NILs) of qSN.A7 were successfully developed by the successive backcross of F1 with Zhongshuang11. First, the effect of qSN.A7 was validated by evaluating the SNPS of two types of homozygous NILs from BC3F2 population, which showed a significant difference of 2.23 on average. Then, qSN.A7 was successfully fine-mapped from the original 4.237 to 1.389 Mb, using a BC4F2 segregating population of 2,551 individuals. To further clarify the regulatory mechanism of qSN.A7, the two types of homologous NILs were subjected to genetic and cytological analyses. The results showed that the difference in SNPS between the two homologous NILs was determined by the embryonic genotypic effect. Highly accordant with this, no significant difference was observed in ovule number per ovary, ovule fertility, fertilization rate, and pollen fertility between the two homologous NILs. Therefore, the regulatory mechanism of qSN.A7 is completely different from the cloned qSS.C9 and qSN.A6. These results will advance the understanding of SNPS and facilitate gene cloning and molecular breeding in Brassica napus.

Introgression Breeding in Cowpea [Vigna unguiculata (L.) Walp.]

The narrow base of genetic diversity characteristic of cowpea can be attributed to it being self-pollinating, evolving from narrow wild germplasm and exhibiting very limited gene flow between wild and cultivated types. Backcrossing to introduce simply inherited desirable traits and utilization of improved breeding lines and varieties as parents in crossing programs further narrowed the genetic base of cowpea varieties. In most cowpea breeding programs, genes for resistance and market traits were pyramided into lines characterized by high levels of acceptance to farmers and consumers. Besides predisposing widely distributed improved varieties to genetic vulnerability, a narrow base of genetic variation may be contributing to the plateauing in cowpea grain yield, which compromises genetic gains. Cross compatible wild relatives have not been used in variety development because breeders shy away from them due to their tiny seed size, unattractive seed coat color and texture, pod shattering, and susceptibility to viruses. A number of wild cowpea relatives, both within and outside section Catiang of Vigna species, have been evaluated for their reaction to cowpea insect pests and diseases. Vigna vexillata lines were resistant to the legume pod borer (Maruca vitrata), the cowpea weevil (Callosobruchus maculatus), and Striga gesnerioides but are cross incompatible with cultivated cowpea. Some lines among the cross compatible wild relative V. unguiculata ssp. dekindtiana were found to be resistant to aphid in the seedling stage, while others showed good levels of drought and heat tolerance. Molecular markers are being generated to identify quantitative trait loci (QTL) with effects on some desirable attributes in cowpea. Modern breeding tools, including transgenics, can be applied for the improvement of cowpea, bypassing the natural barriers of traditional breeding. Transgenic cowpea with Bt gene cry1Ab showing resistance to M. vitrata has been released in Nigeria. Genome editing, a powerful emerging tool, can also be used for developing improved cowpea varieties with durable resistance to pests and diseases.

Temporal genetic patterns of root growth in Brassica napus L. revealed by a low-cost, high-efficiency hydroponic system

Application of a low-cost and high-efficiency hydroponic system in a rapeseed population verified two types of genetic factors ("persistent" and "stage-specific") that control root development. The root system is a vital plant component for nutrient and water acquisition and is targeted to enhance plant productivity. Genetic dissection of the root system generally focuses on a single stage, but roots grow continuously during plant development. To reveal the temporal genetic patterns of root development, we measured nine root-related traits in a rapeseed recombinant inbred line population at six continuous stages during vegetative growth, using a modified hydroponic system with low-cost and high-efficiency features that could synchronize plant growth under controlled conditions. Phenotypic correlation and growth dynamic analysis suggested the existence of two types of genetic factors ("persistent" and "stage-specific") that control root development. Dynamic (unconditional and conditional) quantitative trait loci (QTL) mapping detected 28 stage-specific and 23 persistent QTLs related to root growth. Among them, 13 early stage-specific, 19 persistent and 8 later stage-specific QTLs were detected at 7 DAS (days after sowing), 16 DAS and 5 EL (expanding leaf stage), respectively, providing efficient and adaptable stages for QTL identification. The effective prediction of biomass accumulation using root morphological traits (up to 96.6% or 92.64% at a specific stage or the final stage, respectively) verified that root growth allocation with maximum root uptake area facilitated biomass accumulation. Furthermore, marker-assistant selection, which combined the "persistent" and "stage-specific" QTLs, proved their effectiveness for root improvement with an excellent uptake area. Our results highlight the potential of high-throughput and precise phenotyping to assess the dynamic genetics of root growth and provide new insights into ideotype root system-based biomass breeding.

Detailed investigation on how the protein corona modulates the physicochemical properties and gene delivery of polyethylenimine (PEI) polyplexes

Given the various cationic polymers developed as non-viral gene delivery vectors, polyethylenimine (PEI) has been/is frequently used in in vitro transfection.

QTL Alignment for Seed Yield and Yield Related Traits in Brassica napus

Worldwide consumption of oil is increasing with the growing population in need for edible oil and the expansion of industry using biofuels. Then, demand for high yielding varieties of oil crops is always increasing. Brassica napus (rapeseed) is one of the most important oil crop in the world, therefore, increasing rapeseed yield through breeding is inevitable in order to cater for the high demand of vegetable oil and high-quality protein for live stocks. Quantitative trait loci (QTL) analysis is a powerful tool to identify important loci and which is also valuable for molecular marker assisted breeding. Seed-yield (SY) is a complex trait that is controlled by multiple loci and is affected directly by seed weight, seeds per silique and silique number. Some yield-related traits, such as plant height, biomass yield, flowering time, and so on, also affect the SY indirectly. This study reports the assembly of QTLs identified for seed-yield and yield-related traits in rapeseed, in one unique map. A total of 972 QTLs for seed-yield and yield-related were aligned into the physical map of B. napus Darmor-bzh and 92 regions where 198 QTLs overlapped, could be discovered on 16 chromosomes. Also, 147 potential candidate genes were discovered in 65 regions where 131 QTLs overlapped, and might affect nine different traits. At the end, interaction network of candidate genes was studied, and showed nine genes that could highly interact with the other genes, and might have more influence on them. The present results would be helpful to develop molecular markers for yield associated traits and could be used for breeding improvement in B. napus.

Genetic and Cytological Analyses of the Natural Variation of Seed Number per Pod in Rapeseed (Brassica napus L.)

Seed number is one of the key traits related to plant evolution/domestication and crop improvement/breeding. In rapeseed germplasm, the seed number per pod (SNPP) shows a very wide variation from several to nearly 30; however, the underlying causations/mechanisms for this variation are poorly known. In the current study, the genetic and cytological bases for the natural variation of SNPP in rapeseed was firstly and systematically investigated using the representative four high-SNPP and five low-SNPP lines. The results of self- or cross-pollination experiment between the high- and low-SNPP lines showed that the natural variation of SNPP was mainly controlled by maternal effect (mean = 0.79), followed by paternal effect (mean = 0.21). Analysis of the data using diploid seed embryo-cytoplasmic-maternal model further showed that the maternal genotype, embryo, and cytoplasm effects, respectively, explained 47.6, 35.2, and 7.5% of the genetic variance. In addition, the analysis of combining ability showed that for the SNPP of hybrid F1 was mainly determined by the general combining ability of parents (63.0%), followed by special combining ability of parental combination (37.0%). More importantly, the cytological observation showed that the SNPP difference between the high- and low-SNPP lines was attributable to the accumulative differences in its components. Of which, the number of ovules, the proportion of fertile ovules, the proportion of fertile ovules to be fertilized, and the proportion of fertilized ovules to develop into seeds accounted for 30.7, 18.2, 7.1, and 43.9%, respectively. The accordant results of both genetic and cytological analyses provide solid evidences and systematic insights to further understand the mechanisms underlying the natural variation of SNPP, which will facilitate the development of high-yield cultivars in rapeseed.

Genetic Dissection of Root Morphological Traits Related to Nitrogen Use Efficiency in Brassica napus L. under Two Contrasting Nitrogen Conditions

As the major determinant for nutrient uptake, root system architecture (RSA) has a massive impact on nitrogen use efficiency (NUE). However, little is known the molecular control of RSA as related to NUE in rapeseed. Here, a rapeseed recombinant inbred line population (BnaZNRIL) was used to investigate root morphology (RM, an important component for RSA) and NUE-related traits under high-nitrogen (HN) and low-nitrogen (LN) conditions by hydroponics. Data analysis suggested that RM-related traits, particularly root size had significantly phenotypic correlations with plant dry biomass and N uptake irrespective of N levels, but no or little correlation with N utilization efficiency (NUtE), providing the potential to identify QTLs with pleiotropy or specificity for RM- and NUE-related traits. A total of 129 QTLs (including 23 stable QTLs, which were repeatedly detected at least two environments or different N levels) were identified and 83 of them were integrated into 22 pleiotropic QTL clusters. Five RM-NUE, ten RM-specific and three NUE-specific QTL clusters with same directions of additive-effect implied two NUE-improving approaches (RM-based and N utilization-based directly) and provided valuable genomic regions for NUE improvement in rapeseed. Importantly, all of four major QTLs and most of stable QTLs (20 out of 23) detected here were related to RM traits under HN and/or LN levels, suggested that regulating RM to improve NUE would be more feasible than regulating N efficiency directly. These results provided the promising genomic regions for marker-assisted selection on RM-based NUE improvement in rapeseed.