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Additional file 1: Figure S1. Identification of new FAX genes in B. napus. We selected genes encoding chloroplast membrane proteins based on significant single-nucleotide polymorphisms (SNPs) associated with biological yield in rapeseed (13/14CQ-BY: 2013/2014Chongqing-biological yield). BnaFAX1-1 (BnaA07g17240D) was closely linked to the significant SNP Bn-A07-p12412116 for biological yield, according to our previous work [30]. Figure S2. Location, structure and conserved motif analysis of FAXs in B. napus. (A) The chromosomal distributions of the BnaFAX genes. (B) Gene structures of BnaFAXs and (C) conserved motifs analysis of BnaFAXs. Figure S3. Expression levels of six members of BnaFAX1 in six tissues of a pair of high- and low-seed oil content accessions grown in Chongqing (CQ24, CQ45) (A, B) and Yunnan (YN24, YN45) (C, D), and the expression levels of BnaFAX1-1 (E), BnaFAX1-2 (F) in seedling leaves (120 days in field) of four pair with high- (HBY) and low-biological yield accessions (LBY). CQ24, YN24 represent high-seed oil content accessions (HO); CQ45, YN45 represent low-seed oil content accessions (LO). St, Stem; Le, Leaf; 30ZP, silique pericarps on the main inflorescence of 30 days after flowering; 30ZS, seeds on the main inflorescence of 30 days after flowering; 30CP, silique pericarps on the primary branch of 30 days after flowering; 30CS, seeds on the primary branch of 30 days after flowering. The expression levels of BnaFAX1-1 (E), BnaFAX1-2 (F) in seedling leaves (120 days in field) of four pair with high- (P281, P542, P125, P257-HBY) and low-biological yield accessions (P319, P276, P131, P81-LBY). The biological yield dry weight per plant for each accession (G). Figure S4. Phytohormone contents in leaves from 32-day-old WT and B. napus lines overexpressing BnaFAX1-1. ABA, abscisic acid; IAA, indole-3-acetic acid; SA, salicylic acid; JA, jasmonic acid. Table S1. Summary of significant associated SNPs and candidate genes for biological yield. Table S2. Chloroplast membrane proteins in candidate intervals associated with biological yield. Table S3. Identification of BnaFAX gene family members. Table S4. List of primer sequences used in this study.

Rapeseed (Brassica napus) is one of the most important oil crops in the world; however, drought significantly curtails its growth and productivity. Identifying drought-tolerant germplasm is an efficient and low-cost strategy for addressing water shortages. Using water loss ratio (WLR) as an index of drought tolerance, we screened a panel of 265 B. napus lines. We identified eight low-WLR and six high-WLR accessions, which were regarded as drought-tolerant and drought-sensitive, respectively. Further validated these selected accessions at the seedling stage under drought-stress conditions. The drought-tolerant accessions had significantly greater fresh and dry weights under drought stress than the drought sensitive accessions. Using RT-qPCR, we showed that a set of previously reported drought-adaptive marker genes were expressed at higher levels in the drought-tolerant lines than in the drought-sensitive lines. These results indicated that the drought-tolerant genotypes could be identified from natural populations using WLR. Then, we performed a genome-wide association study to identify loci harboring single nucleotide polymorphisms (SNPs). A total of 139 SNPs were significantly associated with the WLR, of which chromosome A10 harbored the largest number. Furthermore, four putative candidate genes were selected by combining the SNP–WLR association results and transcriptional expression data with the changes in drought tolerance. Thus, we have identified two drought-tolerant B. napus cultivars and uncovered genome-wide variation differentiating B. napus lines related to WLR, in addition to providing insights for further research into WLR-related drought mechanisms.

Genes in the major histocompatibility complex (MHC, also known as HLA) play a critical role in the immune response and variation within the extended 4-Mb region shows association with major risks of many diseases. Yet, deciphering the underlying causes of these associations is difficult because the MHC is the most polymorphic region of the genome with a complex linkage disequilibrium structure. Here, we reconstruct full MHC haplotypes from de novo assembled trios without relying on a reference genome and perform evolutionary analyses. We report 100 full MHC haplotypes and call a large set of structural variants in the regions for future use in imputation with GWAS data. We also present the first complete analysis of the recombination landscape in the entire region and show how balancing selection at classical genes have linked effects on the frequency of variants throughout the region.

Expansive soils are widely distributed in southwest of China and are used frequently in highway construction. The stability of protection mode for expansive soil cutting slope is widely concerned by engineers. Through a large number of field research, laboratory tests, test section construction and monitoring, especially the use of statistical analysis, this research identified the most suitable protection mode is arch skeleton for expansive soil cutting slope of highway. According to the logistic regression, t-test, and other statistical analysis results, this study concluded that the slope stability rate reached 86.84% after protection with arch skeleton. Therefore, arch skeleton is significantly better than other modes of protection, p=0.0581. In addition, this study found that the height and slope rate had a great influence on the stability of expansive soil cutting slope. It is recommended that the slope rate of expansive soil cutting slope should not be steeper than 1:1.5 and the slope height should not exceed 6m.

Clearing the engineering characteristics of high plastic clay and its engineering application are the basis for rational use of high plastic clay to fill the embankment. In this study, a series of water content tests, relative density tests, liquid and plastic limit tests, the grain size analysis tests, compaction and California Bearing Ratio (CBR) tests were carried out based on high plastic clay of diseased subgrade along west-section of Hainan Beltline Freeway. The relationships between CBR and water content, coarse particle content and compaction energy were studied. The results indicated that water content, coarse particle content, and compaction energy had significant effect on CBR, and water content is the main impact factor on CBR values. The maximum CBR water content was greater than the optimal water content by 4% to 5%. The performance of CBR and dry density had obvious distinction under different consistency and compaction energy. The equilibrium water content of high plastic clay subgrade during highway running period was near the plastic limit, which is 6% to 13% higher than the optimal water content. Base on the indoor test results, the problems related to the application of high plastic clay in subgrade filling were analyzed considering the characteristics of highway engineering and climate in Hainan province. It was concluded that high plastic clay could be directly used for embankment filling when the compaction energy conducted under the maximum CBR water content.

BACKGROUND: The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transplantation. The cost and technical limitations of current laboratory techniques, together with advances in next-generation sequencing (NGS) methodologies, have increased the need for precise computational typing methods.RESULTS: We tested two widespread HLA typing methods using high quality full genome sequencing data from 150 individuals in 50 family trios from the Genome Denmark project. First, we computed descendant accuracies assessing the agreement in the inheritance of alleles from parents to offspring. Second, we compared the locus-specific homozygosity rates as well as the allele frequencies; and we compared those to the observed values in related populations. We provide guidelines for testing the accuracy of HLA typing methods by comparing family information, which is independent of the availability of curated alleles.CONCLUSIONS: Although current computational methods for HLA typing generally provide satisfactory results, our benchmark - using data with ultra-high sequencing depth - demonstrates the incompleteness of current reference databases, and highlights the importance of providing genomic databases addressing current sequencing standards, a problem yet to be resolved before benefiting fully from personalised medicine approaches HLA phenotyping is essential.