Identification and characterization of genomic DNA sequences of the S-ribonuclease gene associated with self-incompatibility alleles S1 to S5 in European pear

The stylar products of the S‐locus for the gametophytic self‐incompatibility (GSI) system in the Rosaceae are ribonucleases (S‐RNases). Recently, sequences for 13 pear S‐RNase alleles have been published and named following a letter–symbol nomenclature (S_a to S_d and S_h to S_p). To establish the correspondence between these sequences and the self‐incompatibility alleles we have described previously (S₁ to S₅), we have amplified genomic DNA with consensus primers from the cultivars, ‘Williams’ (S₁S₂), ‘Coscia’ (S₃S₄), ‘Butirra Precoce Morettini’ (S₁S₃), ‘Santa Maria Morettini’ (S₂S₃) and ‘Doyenne du Comice’ (S₄S₅) and identified PCR products specifically associated with each S allele. Cloning and sequencing of the amplification products has revealed that they correspond to European pear sequences already deposited in the database. This allowed us to link S‐RNase sequences with S allele phenotypes and to determine a correspondence between the symbol–letter nomenclature used to name S‐RNase sequences and the number‐based nomenclature used to name S alleles. Based on this result the prediction of new cross‐incompatibilities among pear cultivars is discussed. Finally, we propose a unified number‐based nomenclature to avoid future confusion denominating S alleles in pear.     

Development of a multiplex allele‐specific primer PCR assay for simultaneous detection of QoI and CAA fungicide resistance alleles in Plasmopara viticola populations

BACKGROUND: DNA‐based diagnosis has become a common tool for the evaluation of fungicide resistance in obligate phytopathogenic fungus Plasmopara viticola. RESULTS: A multiplex allele‐specific primer PCR assay has been developed for the rapid detection of fungicide resistance in P. viticola populations. With this assay, a glycine‐to‐alanine substitution at codon 143 of the P. viticola cytochrome b gene, which conferred QoI fungicide resistance, and a glycine‐to‐serine substitution at codon 1105 of the P. viticola cellulose synthase gene PvCesA3, which conferred CAA fungicide resistance, were detected simultaneously. CONCLUSION: It is suggested that the present assay is a reliable tool for the rapid and simultaneous detection of QoI and CAA fungicide resistance alleles in P. viticola populations. The assay required only 2 h from the sampling of symptoms to the detection of resistance alleles to both fungicides. Copyright © 2012 Society of Chemical Industry     

几对麦谷蛋白亚基对小麦面筋品质的影响

麦谷蛋白亚基组成类型是决定小麦加工品质的重要内在因素,改进小麦品种的亚基构成已成为品质育种的重要依据之一,因而鉴定优质亚基的类型对品质育种具有重要的意义.本研究采用郑麦9023/安农9267、皖麦19/安农9267/皖麦19、#445/陕225//安农91168/繁3/皖麦19的F5代株系,烟农19/安农9914、烟农19/安农9916的F3代株系,烟农19/安农9914的F4株系组成9个群体,共1 562个株系,分别检测HMW-GS、LMW-GS的组成,测定了和面图参数和SDS沉降值,分析了麦谷蛋白亚基等位基因对品质性状的影响.结果表明,在Glu-A1位点,1亚基的SDS沉降值显著高于N亚基,1亚基的峰高显著大于N亚基,对于和面时间、衰落角(耐揉性),两亚基间差异不显著.在Glu-D1位点,5 10亚基SDS沉降值显著高于2 12,和面图参数中峰高及和面时间5 10显著高于2 12,衰落角差异不明显;2 12亚基与4 12亚基对SDS沉降值及和面图参数的影响差异不显著.Glu-B1位点,SDS沉降值17 18亚基高于14 15亚基,峰高与衰落角两对亚基间差异不显著,和面时间17 18亚基显著高于14 15亚基;对于LMW-GS,Ⅱ-1群体的Glu-D3e亚基SDS沉降值显著高于Glu-D3a,其他3个群体亚基间差异不显著,在和面时间、峰高及衰落角3项指标中,Glu-D3a与Glu-D3e间差异不显著.     

鲤饲料转化率性状的关联分析及优异等位变异挖掘

饲料转化率是鲤养殖重要的亟待改良的经济性状之一。本研究利用分布于鲤全基因组的1 536个SNP标记,分析68尾全同胞家系镜鲤Cyprinus carpio的基因分型,采用TASSEL软件的GLM和MLM模型检测与饲料转化率性状紧密关联的标记位点,发掘相关位点内的优异等位变异。本研究共获得17个与饲料转化率性状显著关联(P0.05)的SNP标记,贡献率在6.4%~16.6%之间,分布于鲤基因组第2、6、11、16、20、32、33、41,和42染色体以及Scaffold1032、1078和2323上,注释了一批饲料转化率相关的候选基因。从显著关联的标记位点内发掘了16种优异等位变异,其平均表型效应值较群体均值高6.2%,较非优势等位变异高12.5%。其中,SNP0919、SNP0167和SNP1016 3个标记的优异等位变异增减效差异最大,暗示这些标记对性状的选择效果明显。本研究发掘的饲料转化率相关的标记及优异等位变异可为鲤饲料转化率性状的分子标记辅助选择及分子设计育种提供依据。     

菜心群体中 AUF2 基因的遗传变异及其与农艺性状的关联分析

【目的】通过检测 Auxin Up-regulated F-box protein2（AUF2）基因在菜心群体中的自然变异，挖掘其优异等位基因，为菜心分子辅助育种提供理论参考。【方法】采用 PCR 扩增后直接测序的方法，检测AUF2 基因在 156 份菜心种质材料中的自然变异，利用 Tassel 5.0 软件的混合线性模型（MLM）对 AUF2 基因的变异位点与菜心群体的株高、单株质量、最大叶长、最大叶宽、最大叶柄长和叶绿素含量（SPAD）等 6 个农艺性状进行关联分析，以期发现显著影响菜心农艺性状的变异位点，并确定其优异等位变异及单倍型。【结果】经测序分析，在 AUF2 基因的 2 996 bp 扩增区域内共检测到 34 个变异位点，构成 36 个单倍型，表现出较高的核苷酸多样性（π = 0.00503）和单倍型多样性（Hd = 0.780），其上游非编码区 1 498 bp 内含 26 个 SNP 和 2 个InDel 位点，编码区 960 bp 内含 5 个 SNP 和 1 个 InDel 位点，而下游非编码区 538 bp 范围没有检测到变异位点。中性检验显示，AUF2 基因在群体中的 Tajima’s D 值、Fu and Li’s D* 值和 Fu and Li’s F* 值均为正值，且显著偏离中性选择，可能是群体平衡选择的结果。经关联分析发现，4 个 SNP 位点与菜心的单株质量、最大叶长、最大叶宽和最大叶柄长等 4 个农艺性状呈显著相关性，其表型解释率在 5.04% ~ 6.52% 范围；4 个优异等位变异构成的单倍型 Hap2 能显著增加菜心的单株质量，极显著地提高最大叶柄长的长度。【结论】AUF2 基因在菜心群体中存在丰富的变异，对菜心的部分农艺性状有显著影响，其优异等位变异和单倍型将有利于菜心品种的遗传改良。     

基于全基因组重测序分析藏猪骨骼肌发育相关基因

为从全基因组水平探索影响藏猪骨骼肌发育的遗传变异，本研究对5头迪庆藏猪进行全基因组重测序，并合并NCBI数据库中来自3个省的藏猪、与藏猪同样小体型及生长慢的巴马香猪、及体型大且生长快速的杜洛克和大白猪共70个猪只的全基因组重测序数据进行整合分析，获得全基因组SNP后结合选择信号检测与等位基因频率(AF)分析鉴定藏猪-香猪与杜洛克-大白猪的遗传差异；利用GO和KEGG功能富集分析藏猪骨骼肌转录组与蛋白组相关基因。结果发现:1)2 211个基因在藏猪-香猪与杜洛克-大白猪2个比较组中存在遗传差异，138个基因富集到骨骼肌发育相关的GO功能集及KEGG通路；2)9个基因(UCHL3、POSTN、COL12A1、PGK1、JPH1、GPT2、RBFOX1、FLNB和DCX)已报道参与藏猪60 d胚胎背最长肌发育调控，1个(CKM)参与6月龄藏猪背最长肌发育调控；3)10个基因共包含936个SNP，其中655个SNP位于基因间区，255个是内含子变异，少量SNP是外显子及调控区变异。本研究从全基因组水平鉴定了与藏猪骨骼肌发育相关基因及其遗传变异，为以后持续深入解析藏猪骨骼肌发育的遗传机制提供参考。