The high‐quality genome of Brassica napus cultivar ‘ZS11’ reveals the introgression history in semi‐winter morphotype

Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi‐winter oilseed rape cultivar ‘ZS11’ and its comprehensive genomic comparison with the genomes of the winter‐type cultivar ‘Darmor‐bzh’ as well as two progenitors. The integrated BAC‐to‐BAC and whole‐genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high‐quality genome assembly of B. napus ‘ZS11’. Within a short evolutionary period (~6700 years ago), semi‐winter‐type ‘ZS11’ and the winter‐type ‘Darmor‐bzh’ maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to ‘Darmor‐bzh’, both two subgenomes of ‘ZS11’ are closely related to its progenitors, and the ‘ZS11’ genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi‐winter‐type ‘ZS11’ underwent potential genomic introgressions with B. rapa (A_r). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization‐responsive flowering time in ‘ZS11’ was first experienced HE, and then underwent genomic introgression event with A_r, which potentially has led to genetic differences in controlling vernalization in the semi‐winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi‐winter oilseed rape in Asia.     

2001—2019年黄土高原植被覆盖度时空演化特征及地理因子解析

探究黄土高原植被覆盖度变化及其与地理因子之间的关系有助于区域植被恢复政策的优化以及人地关系的协调发展。因此,以MOD13 A1数据作为数据基础,采用趋势分析、标准差和重心迁移模型,研究2001—2019年黄土高原植被覆盖度FVC(Fractional Vegetation Cover)时空演化特征,并结合地理探测器和相关分析对影响FVC的地理因子进行解析。结果表明：(1)2001—2019年黄土高原植被覆盖度恢复状况较好,FVC平均增速为0.0095/a,呈东南高西北低分布,极显著、显著增加的区域面积占比为84.37%,研究区各年FVC重心位于陕北一带,19年向北推进55.1km;(2)各地理因子对FVC的解释力存在显著差异,降水、土壤类型、气温、土地利用类型和坡度是FVC空间分布的主要驱动因子,且各因子之间交互作用的解释力高于单因子;(3)FVC与气温、降水相关系数均以正相关为主;FVC均值与变化趋势存在地形、土壤、人口密度、土地利用分异特征;土地利用转移可体现人类活动特征,其退耕还林还草、未利用地绿化等积极效应促使区域植被得到显著改善,城市扩张等消极效应则抑制植被增长。     

Analysis of QTLs for erucic acid and oil content in seeds on A8 chromosome and the linkage drag between the alleles for the two traits in Brassica napus

The history of canola breeding began with the discovery of germplasm with low erucic acid content in seeds of spring forage cultivar in the 1950's.FAE1 mutations led to a dramatic decrease of the seed erucic acid content in Arabidopsis thaliana.The products of the two FAE1 loci,BnA8.FAE1 and BnC3.FAE1,showed additive effects to the level of erucic acid content in oilseed rape.Previous research believed that the pleiotropy of FAE1 was responsible for the decrease in seed oil content along with the reduction ...     

Analysis of QTLs for emcic acid and oil content in seeds on A8 chro- mosome and the linkage drag between the alleles for the two traits in Brassica napus

The history of canola breeding began with the discovery of germplasm with low erucic acid content in seeds of spring forage cultivar in the 1950's. FAE1 mutations led to a dramatic decrease of the seed erucic acid content in Arabidopsis thaliana. The products of the two FAE1 loci, BnA8.FAE1 and BnC3.FAE1, showed additive effects to the level of erucic acid content in oilseed rape. Previous research believed that the pleiotropy of FAE1 was responsible for the decrease in seed oil content along with the reduction of seed erucic acid content in the modern cultivars. TN DH population was developed from a canola cultivar Tapidor and a Chinese traditional cultivar Ningyou7. The population had been tested in 10 and 11 environments to map QTLs for the erucic acid content and oil content in seeds. As the map resolution increased, a novel QTL for seed erucic acid content was revealed, after Meta-analysis, 7 cM away from the most significant seed erucic acid content QTL where BnA8.FAE1 is located. Seven independent QTLs for seed oil content (qOC) were detected around the two seed erucic acid content QTLs (qEA) across 39.20 cM on linkage group A8. Two of the qOCs co-localized with the two qEAs, respectively, and were detected in a single environment. The other five qOCs were detected in 10 of 11 environments independent of qEAs. Alleles from Tapidor in all the QTLs at the 0–39.20 cM region contributed negative effects to either erucic acid content or oil content in seeds. Parallel, genotyping showed that on 5 of the 7 QTLs regions, Tapidor alleles had the same genotypes with that in ‘Liho’, the original low seed erucic acid content source. Through rounds of crossbreeding with oil-cropped cultivars and intensive selection for multi generations, Tapidor still had the inferior alleles for low seed oil content from ‘Liho’, the forage rape. This showed a strong linkage drag of low seed oil content, which was controlled by the five qEA-independent qOCs, with low seed erucic acid content. Ninety cultivars of B. napus from 8 countries were used to analyze the genetic drag with 9 molecular markers located in the QTL confidence intervals (24.04 cM) on linkage group A8. It was noticed that more than 46% of the cultivars with low seed erucic acid content trait remained the genotype of low seed oil content at least in one locus. Backcross and marker-assisted selection could break the genetic drag between the low oil content and erucic acid in seeds in the process for breeding modern high seed oil content canola cultivars.     

The acyl-homoserine lactone (AHL)-type quorum sensing system affects growth rate,swimming motility and virulence in <Emphasis Type="Italic">Acidovorax avenae</Emphasis> subsp. <Emphasis Type="Italic">citrulli</Emphasis>

Acidovorax avenae subsp. citrulli is a Gram-negative bacterium and is the causal agent of bacterial fruit blotch (BFB) in cucurbits. In this study, the role played by the acyl-homoserine lactone (AHL)-type quorum sensing (QS) system in growth, swimming motility and virulence was characterized in A. avenae subsp. citrulli strain XJL12. The AHL synthase gene of the QS system from strain XJL12, defined as aacI, was cloned and characterized, and an aacI disruption mutant was generated. The aacI mutant XJL13 abolished the ability to produce AHL molecules, whereas the corresponding complemented strain CPXJL13 produced wild-type levels of AHL. The aacI mutant exhibited a significant decrease in growth rate relative to the wild type in minimal medium, and was partially impaired in swimming motility. In plants, the aacI mutant showed a significant reduction of virulence in watermelon fruits and melon seedlings when compared to the wild-type strain. However, the aacI mutation in strain XJL12 had no effects on biofilm formation, exopolysaccharide production, or induction of hypersentitive response in Nicotiana tabacum. Our data suggest that the AHL-type QS may play a key role in pathogen virulence and this may provide an opportunity to explore novel approaches for managing BFB in cucurbits by QS interference.     

A dynamic and complex network regulates the heterosis of yield-correlated traits in rapeseed (Brassica napus L.)

Although much research has been conducted, the genetic architecture of heterosis remains ambiguous. To unravel the genetic architecture of heterosis, a reconstructed F(2) population was produced by random intercross among 202 lines of a double haploid population in rapeseed (Brassica napus L.). Both populations were planted in three environments and 15 yield-correlated traits were measured, and only seed yield and eight yield-correlated traits showed significant mid-parent heterosis, with the mean ranging from 8.7% (branch number) to 31.4% (seed yield). Hundreds of QTL and epistatic interactions were identified for the 15 yield-correlated traits, involving numerous variable loci with moderate effect, genome-wide distribution and obvious hotspots. All kinds of mode-of-inheritance of QTL (additive, A; partial-dominant, PD; full-dominant, D; over-dominant, OD) and epistatic interactions (additive × additive, AA; additive × dominant/dominant × additive, AD/DA; dominant × dominant, DD) were observed and epistasis, especially AA epistasis, seemed to be the major genetic basis of heterosis in rapeseed. Consistent with the low correlation between marker heterozygosity and mid-parent heterosis/hybrid performance, a considerable proportion of dominant and DD epistatic effects were negative, indicating heterozygosity was not always advantageous for heterosis/hybrid performance. The implications of our results on evolution and crop breeding are discussed.     

胡萝卜软腐果胶杆菌鞭毛钩基因flgK 的功能

【目的】为了研究鞭毛钩基因flgK在胡萝卜软腐果胶杆菌胡萝卜亚种(Pectobacterium carotovorum subsp.carotovorum,P.c.c)的功能。【方法】本研究采用两亲同源交换法构建了基因缺失突变体ΔflgKpcc并构建了互补菌株ΔflgKpcc-KH,测定突变体及其互补菌株的菌体形态、运动性、致病因子、致病性等表型。【结果】与野生菌株PccS1相比,ΔflgKpcc鞭毛缺失,菌体易沉降,在0.3%半固体培养基上运动能力明显降低,生长速率无明显变化,但是纤维素酶和蛋白酶的活性、生物膜形成能力明显下降,对感病寄主的致病力显著减弱。基因互补可以使上述突变表型恢复。【结论】实验表明,鞭毛基因flgK突变导致了菌体的运动性降低、病原菌毒性相关的酶活力下降,从而导致致病力下降。     

Ss‐Rhs1, a secretory Rhs repeat‐containing protein,is required for the virulence of Sclerotinia sclerotiorum

Sclerotinia sclerotiorum is a devastating necrotrophic plant pathogen with a worldwide distribution. Cell wall‐degrading enzymes and oxalic acid are important to the virulence of this pathogen. Here, we report a novel secretory protein, Ss‐Rhs1, which is essential for the virulence of S. sclerotiorum. Ss‐Rhs1 is believed to contain a typical signal peptide at the N‐terminal and eight rearrangement hotspot (Rhs) repeats. Ss‐Rhs1 exhibited a high level of expression at the initial stage of sclerotial development, as well as during the hyphal infection process. Targeted silencing of Ss‐Rhs1 resulted in abnormal colony morphology and reduced virulence on host plants. Microscopic observations indicated that Ss‐Rhs1‐silenced strains exhibited reduced efficiency in compound appressoria formation.     

Mapping of genetic locus for leaf trichome in <Emphasis Type="Italic">Brassica oleracea</Emphasis>

Key message

The genetic locus for leaf trichome was identified via marker-based mapping and SNP microarray assay, and a functional marker was developed to facilitate the breeding for hairiness in Brassica oleracea.

Abstract

Plant trichomes are involved in various functions particularly in protecting plants against some biotic and abiotic damages. In the present study, an F2 segregating population was developed from the cross between a glabrous cultivated B. oleracea (CC, 2n = 18) and a hairy wild relative, B. incana (CC, 2n = 18). A 1:3 segregation pattern between glabrous and hairy plants was detected among 1063 F2 genotypes, and the locus for hairiness was mapped in a 4.3-cM genetic region using 267 SSR markers among 149 F2 genotypes, corresponding to a 17.6-Mb genomic region on chromosome C01. To narrow the genetic region for hairiness, the Brassica 60 K SNP Bead Chip Arrays were applied to genotype 64 glabrous and 30 hairy F2 plants, resulting in a 1.04-Mb single peak region located in the 17.6-Mb interval. A candidate gene, BoTRY, was identified by qRT-PCR which revealed significant higher expression in glabrous F2 genotypes as compared with that in hairy plants. A cleaved amplified polymorphic site marker was successfully developed to distinguish the sequence variations of BoTRY between hairy and glabrous plants. Our study will be helpful for molecular breeding for hairiness in B. oleracea.