Genome-Wide Association Studies of Salt Tolerance at Seed Germination and Seedling Stages in Brassica napus

Functional genomics of Brassica napus: Progresses, challenges, and perspectives

Brassica napus, commonly known as rapeseed or canola, is a major oil crop contributing over 13% to the stable supply of edible vegetable oil worldwide. Identification and understanding the gene functions in the B. napus genome is crucial for genomic breeding. A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in B. napus. In this review, we present an overview of the progress made in the functional genomics of B. napus, including the availability of germplasm resources, omics databases and cloned functional genes. Based on the current progress, we also highlight the main challenges and perspectives in this field. The advances in the functional genomics of B. napus contribute to a better understanding of the genetic basis underlying the complex agronomic traits in B. napus and will expedite the breeding of high quality, high resistance and high yield in B. napus varieties.

Identification candidate genes for salt resistance through quantitative trait loci-sequencing in Brassica napus L

Rapeseed (Brassica napus L.) is one of the most important oil crops worldwide. However, its yield is greatly limited by salt stress, one of the primary abiotic stresses. Identification of salt-tolerance genes and breeding salt-tolerant varieties is an effective approach to address this issue. Unfortunately, little is known about the salt-tolerance quantitative trait locus (QTL) and the identification of salt tolerance genes in rapeseed. In this study, high-throughput quantitative trait locus sequencing (QTL-seq) was applied to identifying salt-tolerant major QTLs based on two DNA pools from an F2:3 population of a cross between rapeseed line 2205 (salt tolerant) and 1423 (salt sensitive). A total of twelve major QTLs related to the salt tolerance rating (STR) were detected on chromosomes A03, A08, C02, C03, C04, C06, C07 and C09. To further enhance our understanding, we integrated QTL-seq data with transcriptome analysis of the two parental rapeseed plants subjected to salt stress, through which ten candidate genes for salt tolerance were identified within the major QTLs by gene differential expression, variation and annotated functions analysis. The marker SNP820 linked to salt tolerance was successfully validated and would be useful as a diagnostic marker in marker-assisted breeding. These findings provide valuable insights for future breeding programs aimed at developing rapeseed cultivars resistant to salt stresses.

Pectin demethylation-mediated cell wall Na+ retention positively regulates salt stress tolerance in oilseed rape

KEY MESSAGE

Integrated phenomics, ionomics, genomics, transcriptomics, and functional analyses present novel insights into the role of pectin demethylation-mediated cell wall Na+ retention in positively regulating salt tolerance in oilseed rape. Genetic variations in salt stress tolerance identified in rapeseed genotypes highlight the complicated regulatory mechanisms. Westar is ubiquitously used as a transgenic receptor cultivar, while ZS11 is widely grown as a high-production and good-quality cultivar. In this study, Westar was found to outperform ZS11 under salt stress. Through cell component isolation, non-invasive micro-test, X-ray energy spectrum analysis, and ionomic profile characterization, pectin demethylation-mediated cell wall Na+ retention was proposed to be a major regulator responsible for differential salt tolerance between Westar and ZS11. Integrated analyses of genome-wide DNA variations, differential expression profiling, and gene co-expression networks identified BnaC9.PME47, encoding a pectin methylesterase, as a positive regulator conferring salt tolerance in rapeseed. BnaC9.PME47, located in two reported QTL regions for salt tolerance, was strongly induced by salt stress and localized on the cell wall. Natural variation of the promoter regions conferred higher expression of BnaC9.PME47 in Westar than in several salt-sensitive rapeseed genotypes. Loss of function of AtPME47 resulted in the hypersensitivity of Arabidopsis plants to salt stress. The integrated multiomics analyses revealed novel insights into pectin demethylation-mediated cell wall Na+ retention in regulating differential salt tolerance in allotetraploid rapeseed genotypes. Furthermore, these analyses have provided key information regarding the rapid dissection of quantitative trait genes responsible for nutrient stress tolerance in plant species with complex genomes.

Graphene oxide decreases the effects of salt stress on Persian clover seed germination

Among biotic and abiotic stresses, the most restrictive for plant distribution is salt stress, where different concentrations might exert harmful effects on seed germination. Recently, nanomaterials were used successfully to mitigate these stresses, indicating that plants may be able to develop normally in adverse conditions. The aim of this study was to examine the effects of graphene oxide (GO) on the germination of Persian clover seedlings under salt stress conditions. Following sown on substrate paper, seeds were tested after exposure to different concentrations of graphene oxide (0, 125, 250, or 500 mg L-1 GO), sodium chloride (0; -0.1; -0.2; -0.3, or -0.4 MPa NaCl) and/or GO + salt concomitantly, and then stored for 7 days in a germination chamber at 20°C in the presence of light. Seed germination and growth parameters of seedlings were determined. Graphene oxide demonstrated protective effect against salt stress as evident by no marked adverse effects on seed germination where GO blocked the salt-induced reduction in germination. The results obtained provide references for the safe application of nanomaterials and emphasize the significance of GO as a promising material for reducing the toxicity of salts in agriculture.

Targeted mutagenesis of BnTTG1 homologues generated yellow-seeded rapeseed with increased oil content and seed germination under abiotic stress

Yellow seed is one desirable trait with great potential to improve seed oil quality and yield. The present study surveys the redundant role of BnTTG1 genes in the proanthocyanidins (PA) biosynthesis, oil content and abiotic stress resistance. Stable yellow seed mutants were generated after mutating BnTTG1 by CRISPR/Cas9 genome editing system. Yellow seed phenotype could be obtained only when both functional homologues of BnTTG1 were simultaneously knocked out. Homozygous mutants of BnTTG1 homologues showed decreased thickness and PA accumulation in seed coat. Transcriptome and qRT-PCR analysis indicated that BnTTG1 mutation inhibited the expression of genes involved in phenylpropanoid and flavonoid biosynthetic pathways. Increased seed oil content and alteration of fatty acid (FA) composition were observed in homozygous mutants of BnTTG1 with enriched expression of genes involved in FA biosynthesis pathway. In addition, target mutation of BnTTG1 accelerated seed germination rate under salt and cold stresses. Enhanced seed germination capacity in BnTTG1 mutants was correlated with the change of expression level of ABA responsive genes. Overall, this study elucidated the redundant role of BnTTG1 in regulating seed coat color and established an efficient approach for generating yellow-seeded oilseed rape genetic resources with increase oil content, modified FA composition and resistance to multiple abiotic stresses.

Two-Component System Genes in Brassica napus: Identification, Analysis, and Expression Patterns in Response to Abiotic and Biotic Stresses

The two-component system (TCS), consisting of histidine kinases (HKs), histidine phosphotransfer proteins (HPs) and response regulators (RRs) in eukaryotes, plays pivotal roles in regulating plant growth, development, and responses to environment stimuli. However, the TCS genes were poorly characterized in rapeseed, which is an important tetraploid crop in Brassicaceae. In this work, a total of 182 BnaTCS genes were identified, including 43 HKs, 16 HPs, and 123 RRs, which was more than that in other crops due to segmental duplications during the process of polyploidization. It was significantly different in genetic diversity between the three subfamilies, and some members showed substantial genetic differentiation among the three rapeseed ecotypes. Several hormone- and stress-responsive cis-elements were identified in the putative promoter regions of BnaTCS genes. Furthermore, the expression of BnaTCS genes under abiotic stresses, exogenous phytohormone, and biotic stresses was analyzed, and numerous candidate stress-responsive genes were screened out. Meanwhile, using a natural population with 505 B. napus accessions, we explored the genetic effects of BnaTCS genes on salt tolerance by association mapping analysis and detected some significant association SNPs/genes. The result will help to further understand the functions of TCS genes in the developmental and stress tolerance improvement in B. napus.

Next-generation bulked segregant analysis for Breeding 4.0

Functional cloning and manipulation of genes controlling various agronomic traits are important for boosting crop production. Although bulked segregant analysis (BSA) is an efficient method for functional cloning, its low throughput cannot satisfy the current need for crop breeding and food security. Here, we review the rationale and development of conventional BSA and discuss its strengths and drawbacks. We then propose next-generation BSA (NG-BSA) integrating multiple cutting-edge technologies, including high-throughput phenotyping, biological big data, and the use of machine learning. NG-BSA increases the resolution of genetic mapping and throughput for cloning quantitative trait genes (QTGs) and optimizes candidate gene selection while providing a means to elucidate the interaction network of QTGs. The ability of NG-BSA to efficiently batch-clone QTGs makes it an important tool for dissecting molecular mechanisms underlying various traits, as well as for the improvement of Breeding 4.0 strategy, especially in targeted improvement and population improvement of crops.

Impacts of salinity stress on crop plants: improving salt tolerance through genetic and molecular dissection

Improper use of water resources in irrigation that contain a significant amount of salts, faulty agronomic practices such as improper fertilization, climate change etc. are gradually increasing soil salinity of arable lands across the globe. It is one of the major abiotic factors that inhibits overall plant growth through ionic imbalance, osmotic stress, oxidative stress, and reduced nutrient uptake. Plants have evolved with several adaptation strategies at morphological and molecular levels to withstand salinity stress. Among various approaches, harnessing the crop genetic variability across different genepools and developing salinity tolerant crop plants offer the most sustainable way of salt stress mitigation. Some important major genetic determinants controlling salinity tolerance have been uncovered using classical genetic approaches. However, its complex inheritance pattern makes breeding for salinity tolerance challenging. Subsequently, advances in sequence based breeding approaches and functional genomics have greatly assisted in underpinning novel genetic variants controlling salinity tolerance in plants at the whole genome level. This current review aims to shed light on physiological, biochemical, and molecular responses under salt stress, defense mechanisms of plants, underlying genetics of salt tolerance through bi-parental QTL mapping and Genome Wide Association Studies, and implication of Genomic Selection to breed salt tolerant lines.

Discovery of common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits in Brassica napus L

KEY MESSAGE

Common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits were identified in Brassica napus combining QTL mapping with transcriptome under salt and alkaline stresses. The yield of rapeseed (Brassica napus L.) is determined by multiple yield-related traits, which are susceptible to environmental factors. Many yield-related quantitative trait loci (QTLs) have been reported in Brassica napus; however, no studies have been conducted to investigate both salt-alkali tolerance and yield-related traits simultaneously. Here, specific-locus amplified fragment sequencing (SLAF-seq) technologies were utilized to map the QTLs for salt-alkali tolerance and yield-related traits. A total of 65 QTLs were identified, including 30 QTLs for salt-alkali tolerance traits and 35 QTLs for yield-related traits, accounting for 7.61-27.84% of the total phenotypic variations. Among these QTLs, 18 unique QTLs controlling two to four traits were identified by meta-analysis. Six novel and unique QTLs were detected for salt-alkali tolerance traits. By comparing these unique QTLs for salt-alkali tolerance traits with those previously reported QTLs for yield-related traits, seven co-localized chromosomal regions were identified on A09 and A10. Combining QTL mapping with transcriptome of two parents under salt and alkaline stresses, thirteen genes were identified as the candidates controlling both salt-alkali tolerance and yield. These findings provide useful information for future breeding of high-yield cultivars resistant to alkaline and salt stresses.

BnIR: A multi-omics database with various tools for Brassica napus research and breeding

In the post-genome-wide association study era, multi-omics techniques have shown great power and potential for candidate gene mining and functional genomics research. However, due to the lack of effective data integration and multi-omics analysis platforms, such techniques have not still been applied widely in rapeseed, an important oil crop worldwide. Here, we report a rapeseed multi-omics database (BnIR; http://yanglab.hzau.edu.cn/BnIR), which provides datasets of six omics including genomics, transcriptomics, variomics, epigenetics, phenomics, and metabolomics, as well as numerous "variation-gene expression-phenotype" associations by using multiple statistical methods. In addition, a series of multi-omics search and analysis tools are integrated to facilitate the browsing and application of these datasets. BnIR is the most comprehensive multi-omics database for rapeseed so far, and two case studies demonstrated its power to mine candidate genes associated with specific traits and analyze their potential regulatory mechanisms.

Identification of a key locus, qNL3.1, associated with seed germination under salt stress via a genome-wide association study in rice

Two causal OsTTL and OsSAPK1 genes of the key locus qNL3.1 significantly associated with seed germination under salt stress were identified via a genome-wide association study, which could improve rice seed germination under salt stress. Rice is a salt-sensitive crop, and its seed germination determines subsequent seedling establishment and yields. In this study, 168 accessions were investigated for the genetic control of seed germination under salt stress based on the germination rate (GR), germination index (GI), time at which 50% germination was achieved (T₅₀) and mean level (ML). Extensive natural variation in seed germination was observed among accessions under salt stress. Correlation analysis showed significantly positive correlations among GR, GI and ML and a negative correlation with T₅₀ during seed germination under salt stress. Forty-nine loci significantly associated with seed germination under salt stress were identified, and seven of these were identified in both years. By comparison, 16 loci were colocated with the previous QTLs, and the remaining 33 loci might be novel. qNL3.1, colocated with qLTG-3, was simultaneously identified with the four indices in two years and might be a key locus for seed germination under salt stress. Analysis of candidate genes showed that two genes, the similar to transthyretin-like protein OsTTL and the serine/threonine protein kinase OsSAPK1, were the causal genes of qNL3.1. Germination tests indicated that both Osttl and Ossapk1 mutants significantly reduced seed germination under salt stress compared to the wild type. Haplotype analysis showed that Hap.1 of OsTTL and Hap.1 of OsSAPK1 genes were excellent alleles, and their combination resulted in high seed germination under salt stress. Eight accessions with elite performance of seed germination under salt stress were identified, which could improve rice seed germination under salt stress.

High-throughput phenotyping-based quantitative trait loci mapping reveals the genetic architecture of the salt stress tolerance of Brassica napus

Salt stress is a major limiting factor that severely affects the survival and growth of crops. It is important to understand the salt stress tolerance ability of Brassica napus and explore the underlying related genetic resources. We used a high-throughput phenotyping platform to quantify 2111 image-based traits (i-traits) of a natural population under three different salt stress conditions and an intervarietal substitution line (ISL) population under nine different stress conditions to monitor and evaluate the salt stress tolerance of B. napus over time. We finally identified 928 high-quality i-traits associated with the salt stress tolerance of B. napus. Moreover, we mapped the salt stress-related loci in the natural population via a genome-wide association study and performed a linkage analysis associated with the ISL population, respectively. These results revealed 234 candidate genes associated with salt stress response, and two novel candidate genes, BnCKX5 and BnERF3, were experimentally verified to regulate the salt stress tolerance of B. napus. This study demonstrates the feasibility of using high-throughput phenotyping-based quantitative trait loci mapping to accurately and comprehensively quantify i-traits associated with B. napus. The mapped loci could be used for genomics-assisted breeding to genetically improve the salt stress tolerance of B. napus.

Genome-Wide Association Studies of Salt Tolerance at the Seed Germination Stage and Yield-Related Traits in Brassica napus L

Salt stress severely affects crop growth and development and reduces the yield of Brassica napus. Exploring natural genetic variations for high salt tolerance in B. napus seedlings is an effective approach to improve productivity under salt stress. Using 10,658 high-quality single nucleotide polymorphic (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, genome-wide association studies (GWAS) were performed to investigate the genetic basis of salt tolerance and yield-related traits of B. napus. The results revealed that 77 and 497 SNPs were significantly associated with salt tolerance and yield-related traits, of which 40 and 58 SNPs were located in previously reported QTLs/SNPs, respectively. We identified nineteen candidate genes orthologous with Arabidopsis genes known to be associated with salt tolerance and seven potential candidates controlling both salt tolerance and yield. Our study provides a novel genetic resource for the breeding of high-yield cultivars resistant to salt stress.

Genome-Wide Association Studies of Salt-Alkali Tolerance at Seedling and Mature Stages in Brassica napus

Most plants are sensitive to salt-alkali stress, and the degree of tolerance to salt-alkali stress varies from different species and varieties. In order to explore the salt-alkali stress adaptability of Brassica napus, we collected the phenotypic data of 505 B. napus accessions at seedling and mature stages under control, low and high salt-alkali soil stress conditions in Inner Mongolia of China. Six resistant and 5 sensitive materials, respectively, have been identified both in Inner Mongolia and Xinjiang Uygur Autonomous Region of China. Genome-wide association studies (GWAS) for 15 absolute values and 10 tolerance coefficients (TCs) of growth and agronomic traits were applied to investigate the genetic basis of salt-alkali tolerance of B. napus. We finally mapped 9 significant QTLs related to salt-alkali stress response and predicted 20 candidate genes related to salt-alkali stress tolerance. Some important candidate genes, including BnABA4, BnBBX14, BnVTI12, BnPYL8, and BnCRR1, were identified by combining sequence variation annotation and expression differences. The identified valuable loci and germplasms could be useful for breeding salt-alkali-tolerant B.napus varieties. This study laid a foundation for understanding molecular mechanism of salt-alkali stress adaptation and provides rich genetic resources for the large-scale production of B. napus on salt-alkali land in the future.