Development of a core set of KASP markers for assaying genetic diversity in Brassica rapa subsp. chinensis Makino

Single‐nucleotide polymorphisms (SNPs) are rapid, economical and reliable genotyping tools. Non‐heading Chinese cabbage (Brassica rapa L. subsp. chinensis Makino) is now an economically important vegetable crop worldwide. In this study, 1,167 SNPs were evaluated for 7polymorphism among 70 representative non‐heading Chinese cabbage inbred lines using a Kompetitive Allele Specific PCR (KASP) genotyping assay. On the basis of identified polymorphisms and the results of a principal component analysis, we selected 50 core SNPs that were balanced sufficiently to provide adequate information for genetic identification. The core SNPs were used for construction of a neighbour‐joining dendrogram that separated the 70 inbred lines into four main groups and several subgroups corresponding to Caixin, Heiyebaicai, Huangxinwu, Naibaicai, Taitsai, Pak‐choi, and Wutatsai. This categorization was superior to that achieved using a dataset of 479 polymorphic SNPs. To confirm the utility of the core SNP markers in genetic identification, we tested their stability and resolution using 162 commercial hybrid cultivars. The SNPs, which represent a cost‐effective, accurate marker set for germplasm analysis and cultivar identification, are suitable for molecular marker‐assisted breeding in non‐heading Chinese cabbage.     

Revisiting rice breeding methods – evaluating the use of rapid generation advance (RGA) for routine rice breeding

Rice production needs to increase in the future in order to meet increasing demands. The development of new improved and higher yielding varieties more quickly will be needed to meet this demand. However, most rice breeding programmes in the world have not changed in several decades. In this article, we revisit the evidence in favour of using rapid generation advance (RGA) as a routine breeding method. We describe preliminary activities at the International Rice Research Institute (IRRI) to re-establish RGA on a large scale as the main breeding method for irrigated rice breeding. We also describe experiences from the early adoption at the Bangladesh Rice Research Institute. Evaluation of RGA breeding lines at IRRI for yield, flowering time and plant height indicated transgressive segregation for all traits. Some RGA lines were also higher yielding than the check varieties. The cost advantages of using RGA compared to the pedigree method were also empirically determined by performing an economic analysis. This indicated that RGA is several times more cost effective and advantages will be realized after 1 year even if facilities need to be built. Based on our experience, and previous independent research empirically testing the RGA method in rice, we recommend that this method should be implemented for routine rice breeding in order to improve breeding efficiency.     

大豆对大豆胞囊线虫侵染的应答机制研究

大豆胞囊线虫病(Heterodera glycines,soybean cyst nematode,SCN)是大豆生产上的重要病害,其特点为危害重、分布广、难防治,每年对大豆生产造成极大的损失。种植大豆抗性新品种是防治SCN目前最为有效的措施,研究大豆对SCN侵染的应答机制,是培育大豆持久抗病品种的前提,对加快抗线虫品种选育及SCN的防控具有重要的意义。本文综述了大豆对SCN侵染的组织细胞学应答机制;介绍了大豆在SCN侵染后酶系变化及酚类代谢的生理生化应答机制;从分子水平阐明了SCN侵染后大豆的基因转录变化,差异蛋白及DNA甲基化的应答机制,以期为大豆胞囊线虫病害的进一步研究与防治提供参考。     

Identification,characterization and full-length sequence analysis of a novel endornavirus in common sunflower (Helianthus annuus L.)

To identify the possible quarantine viruses in seven common sunflower varieties imported from the United States of America and the Netherlands, we tested total RNAs extracted from the leaf tissues using next-generation sequencing of small RNAs. After analysis of small RNA sequencing data, no any quarantine virus was found, but a double-stranded RNA(dsRNA) molecule showing typical genomic features of endornavirus was detected in two varieties, X3939 and SH1108. Full-length sequence and phylogenetic analysis showed that it is a novel endornavirus, temporarily named as Helianthus annuus alphaendornavirus(HaEV). Its full genome corresponds to a 14 662-bp dsRNA segment, including a 21-nt 5′ untranslated region(UTR), 3' UTR ending with the unique sequence CCCCCCCC and lacking a poly(A) tail. An open reading frame(ORF) that encodes a deduced 4 867 amino acids(aa) polyprotein with three domains: RdRP, Hel and UGT(UDP-glycosyltransferase). HaEV mainly distributed in the cytoplasm but less in the nucleus of leaf cells by fluorescence in situ hybridization(FISH) experiment. This virus has a high seed infection rate in the five varieties, X3907, X3939, A231, SH1108 and SR1320. To our knowledge, this is the first report about the virus of the family Endornaviridae in the common sunflower.     

Establishing an eyeball-weight relationship for Litopenaeus vannamei using machine vision technology

This study aimed to establish a shrimp eyeball-weight relationship model for Litopenaeus vannamei using machine vision technology. A total of 295 shrimp were sampled from a recirculating aquaculture system (RAS). The long-axis length (d), body length (L), and body weight (W) of each individual was measured. The long axis length of the shrimp eyeball was identified and measured using machine vision technology. Continuous fitting and piecewise fitting models were used to construct the eyeball-weight relationship model for L. vannamei. The continuous fitting relationship model was described as: W = 38.865d^2.7914, while the piecewise model was described as: d < 2 mm, W = 0.0326d^3.7363, R² = 0.9288; 2 mm ≤ d < 3.9 mm, W = 0.0401d^3.104, R² = 0.9629; 3.9 mm ≤ d < 5.8 mm, W = 0.0421d^3.0311, R² = 0.9216; 5.8 mm < d, W = 0.103d^2.6226, R² = 0.9457. The root mean square error (RMSE) of the piecewise fitting model (0.0244, 0.1575, 0.5034, 0.7072) was smaller than the continuous fitting model (0.8229). The correlation coefficient (R²) of the piecewise model (0.9288, 0.9629, 0.9216, and 0.9457) was similar to that of the continuous fitting model (R² = 0.9621). The results indicated that the piecewise fitting model is suitable for calculating the biomass of L. vannamei in RAS and provides a novel way of estimating the biomass of L. vannamei cultured in RAS. The piecewise fitting model can also provide the foundation of evaluating the production of shrimp using underwater image recognition in intelligent aquaculture systems.     

一种基于RPA的番茄褪绿病毒检测方法

番茄褪绿病毒Tomato chlorosis virus(ToCV)引起番茄褪绿病毒病,给番茄生产造成严重危害。开发快速准确的检测方法对该病害的防控具有重要意义。利用番茄褪绿病毒外壳蛋白(CP)基因序列,设计特异性引物,建立了ToCV的重组酶聚合酶等温扩增(recombinase polymerase amplification, RPA)检测方法,同时分析了该方法的灵敏度和特异性。结果表明,建立的ToCV-RPA方法在38℃恒温下40 min可从ToCV阳性的番茄样品中扩增出246 bp的特异性条带。扩增时间短,对设备要求低,且与番茄其他病毒无交叉反应,特异性好,灵敏度可达到PCR方法的10倍,适用于ToCV的快速检测。     

胡麻脂肪酸去饱和酶基因(fads)差异表达分析

为了了解fad基因在胡麻蒴果发育过程中对不饱和脂肪酸的调控,对高、中、低三个不同亚麻酸(C18:3)含量的胡麻品种(’CDC Gold’,‘内亚7号’,’Linola’)进行了不同时期的品质测定,以及脂肪酸去饱和酶2a基因(fad2a)、脂肪酸去饱和酶2b基因(fad2b)、脂肪酸去饱和酶2c基因(fad2c)、脂肪酸去饱和酶3a基因(fad3a)、脂肪酸去饱和酶3b基因(fad3b)的qRT-PCR定量分析。结果表明,随着蒴果成熟,可溶性糖含量呈降低趋势,粗脂肪与粗蛋白不断积累,且差异显著(p<0.05)。fad2a基因、fad3a基因以及fad3b基因在各个时期中的表达符合正态分布。以0 d的蒴果为对照,在胡麻种子形成过程中,‘内亚7号’的三个基因在5 d和15 d的表达量迅速增加,到30 d时急剧减少,15 d的fad2a基因表达量为5.23倍,fad3a基因表达量是fad2a基因表达量的14.52倍,fad3b基因的表达量是fad2a基因表达量的16.14倍,表明这三个基因参与不饱和脂肪酸积累过程。在低亚麻酸含量品种‘Linola’30 d中,fad3a基因是fad2a基因表达量的52.71倍,fad3b呈下调趋势;在高亚麻酸含量品种‘CDCGold’30d中,fad3a基因与fad2a基因的表达量均呈下调趋势,fad3b的表达量为3.92倍;在中等亚麻酸含量品种‘内亚7号’中,fad2a基因表达量降低了0.31倍,fad3a基因是fad3b基因表达量的1.87倍。fad2b基因、fad2c基因熔解曲线不稳定,峰值低,可以在后续试验中继续探索。     

鄂托克前旗近50年降水变化特征分析

本文利用鄂托克前旗1967-2018年气象观测站近50年的气象资料,对鄂托克前旗降水特征进行分析。结果表明：整体来说，鄂托克前旗的年降水量变化呈现微弱降低趋势，每10a大约减少1.2mm；28a时间尺度决定的主周期控制着该地区的年降水变化特征，通过周期和突变分析，预计未来三年左右降水高于多年平均值，随后的14年左右时间内降水量呈现减少趋势，逐渐低于多年平均降水量。     

A genetic linkage map in southern‐by‐spring oat identifies multiple quantitative trait loci for adaptation and rust resistance

We developed 178 recombinant inbred lines from a southern‐by‐spring oat population designated as “TxH.” These lines were genotyped to generate a high‐quality linkage map that resolved 6,902 markers into 21 linkage groups that matched closely with the latest hexaploid oat consensus map. Three major quantitative trait loci (QTLs) affecting heading date were found in locations that are consistent with known QTLs and candidate genes, and two other QTLs affecting heading date were found in novel locations. Five QTLs affecting plant height were found. Both sets of QTLs are responsible for transgressive segregation observed for these two traits. Four QTLs affecting resistance to crown rust, caused by the pathogen Puccinia coronata f. sp. avenae, were identified. Two of these QTLs are consistent with known clusters of rust resistance genes, while two may represent new locations of novel rust resistance genes. A complete set of SNP sequences suitable for generating markers for molecular selection is provided.     

Influence of soil phosphorus status,texture, pH and metal content on the efficacy of amendments to pig slurry in reducing phosphorus losses

Cost‐effective strategies for using chemically amended organic fertilizers need to be developed to minimize nutrient losses in surface and groundwater. Coupling specific soil physical and chemical characteristics with amendment type could increase their effectiveness. This study investigated how water‐extractable phosphorus (P) was affected by chemical amendments added to pig slurry and how this effect varied with soil properties. A 3‐month incubation study was conducted on 18 different mineral soils, stored at 10 °C and 75% humidity and treated with unamended and amended slurry which was incorporated at a rate equivalent to 19 kg total P (TP )/ha. The amendments examined were commercial‐grade liquid alum, applied at a rate of 0.88:1 [Al:TP ], and commercial‐grade liquid poly‐aluminium chloride (PAC ), applied at a rate of 0.72:1 [Al:TP ]. These amendments were previously identified by the authors as being effective in reducing incidental losses of P. The efficacy of the amendments varied with the soil test P, the degree of P saturation (DPS ) and the Mehlich aluminium, iron and calcium, but not soil texture. Chemical amendments were most effective in soils with DPS over approximately 20%. Due to their high cost, the incorporation of amendments into existing management practices can only be justified as part of a holistic management plan where soils have high DPS .