Identification of the putative ancestral allele of bovine single‐nucleotide polymorphisms

Identifying the action of natural selection from patterns of standing genetic variation has long been of interest to the population genetic community. Thanks to the availability of large single‐nucleotide polymorphism (SNP) data sets for many species and of high‐throughput SNP genotyping methods, whole‐genomic surveys to detect selective sweeps are now possible. Knowing the ancestral allele increases the power to detect selection. We present here a comparative genomic approach to determine the putative ancestral allele of bovine SNPs deposited in public databases. We analysed 19 551 488 SNPs and identified the putative ancestral allele for 14 339 107 SNPs. Our predicted ancestral alleles were in agreement with ancestral alleles detected by genotyping outgroup species for 97% SNPs from the BovineSNP50 BeadChip. This comparison indicates that our comparative genomic‐based approach to identify putative ancestral alleles is reliable.     

水稻矮秆突变体Zj88d的鉴定与基因定位

 用甲基磺酸乙酯诱变处理常规粳稻浙粳88,获得了矮秆水稻突变体Zj88d,多代自交稳定遗传。遗传分析表明突变体Zj88d的矮秆性状受一对隐性核基因控制。采用图位克隆方法,将目的基因定位在水稻第7染色体短臂末端7 44w和RM5344间的603 kb区间。排查该区间包含的100个候选基因,发现已克隆的矮秆基因OSH15也位于其中。测序结果显示,突变体Zj88d中的OSH15基因在第2内含子最末位发生“g→a”单碱基突变。     

Genetical control of alkaloid production in Lupinus mutabilis and the effect of a mutant allele Mutal isolated following chemical mutagenesis

Summary A new mutant allele, described here as mutal, which reduces the alkaloid content in dry matter of lupinus mutabilis has been identified following seed treatment with ethyl methane sulphanate. The allele, when homozygous, reduces the alkaloid content from levels of > 2.0 per cent found in seed dry matter of existing populations to 0.2–0.3 per cent and produces plants with vegetative and seed tissues that are organoleptically sweet. Component alkaloids in plants homozygous for mutal differ in respect of the percentage composition of sparteine and of lupanine, as well as possibly of oxa-sparteine and 4-hydroxylupanine, but none is eliminated in genotypes homozygous for the mutant allele. Alkaloid concentration, in so far as not under the control of mutal, has low heritability but lines were isolated following two generations of successive selection which possessed reduced alkaloid levels. These were interpreted to have arisen as a result of recombination of alleles affecting reduction in alkaloid level at several loci. the mutant, mutal, has been established in a pure breeding line which represents a crucial additional step in the evolution of Lupinus mutabilis towards full status as a crop plant.     

Isozyme polymorphism in three gene pools of cultivated chicory (Cichorium intybus L.)

Summary Polymorphism of ten enzymes, acid phosphatase (APH), isocitrate dehydrogenase (IDH), leucine aminopeptidase (LAP), phosphorylase (PP), superoxide dismutase (SOD), malic enzyme (ME), glutamate oxaloacetate transaminase 1 and 2 (GOT-1, GOT-2) and phosphoglucomutase 1 and 2 (PGM-1 and PGM-2), was investigated in three gene pools of cultivated chicory, including six cultivated wild chccory, eight industrial chicory and eight Brussels chicory varieties. LAP, APH, PP and PGM-2 showed high phenotypic polymorphism whilst GOT-1 and ME had poor polymorphism. For three enzyme coding loci Lap, Pgm-1 and Got-2, allele frequencies were determined. Isozyme composition in the three chicory gene pools was significantly different, showing, respectively, high, intermediate and poor average amount of phenotypic polymorphism in cultivated wild chicory, industrial chicory and Brussels chicory. Isozyme variation within and between varieties of the three gene pools is discussed in relation to breeding practices.     

S‐locus diversity and cross‐compatibility of wild Prunus avium for timber breeding

Prunus avium is primarily cultivated for its fruit, sweet cherries. However, it is also used to produce high‐quality timber. In a P. avium seed orchard, gametophytic self‐incompatibility is a restriction for free pollen flow and should be considered when establishing basic forest materials. In this study, S‐locus diversity and cross‐incompatibility of wild cherry individuals in clonal banks established for breeding for timber production were investigated. Wild cherry trees (140) with outstanding forest growth habit, collected in northern Spain, grafted and planted in two clonal banks, were genotyped at the S‐locus. The self‐incompatibility S‐locus genes, S‐RNase and SFB, were analysed by PCR. Twenty‐two S‐haplotypes, resulting in 72 different S‐genotypes, were identified. The genotypes were grouped into 33 incompatibility groups and 39 unique genotypes. This initial S‐locus analysis revealed large genetic diversity of wild cherry trees from the Spanish northern deciduous forest, and provides useful information for seed orchard design. Wild P. avium displays significantly more genetic diversity than what is detected in local cultivars, revealing a narrowing of genetic diversity during local domestication.     

中国栽培和野生大豆农艺及品质性状与SSR标记的关联分析 II. 优异等位变异的发掘

在前文研究已检出与农艺品质性状显著关联的SSR位点的基础上, 本文进一步对与性状关联位点的等位变异作解析, 通过将携带某等位变异的所有材料表型均值与携带无效等位基因(null allele)材料表型均值做比较, 估计等位变异的潜在表型效应增量(减量), 进一步利用该信息估计位点增效(减效)等位变异的平均效应, 鉴别出一批农艺品质性状优异位点、等位变异及携带优异等位变异的载体材料。发现在栽培及野生种质中检出的优异等位变异有同、有异、有互补性。发现关联位点正、负效应等位变异均值间有差异, 可根据育种目标性状选择要求, 选取适合的位点及相应等位变异。同一标记位点可与多性状关联, 其等位变异在不同性状间各有其表型效应的方向和大小; 等位变异在相关性状效应上方向、大小的异同解释了性状间正、负相关的遗传原因。关联作图得到的信息可以弥补家系连锁法QTL定位信息的不足, 并直接利用等位变异信息进行亲本选拔、组合选配及后代等位条带辅助选择以提高育种成效。     

水稻耐盐碱胁迫优异等位变异的发掘

本研究以281个水稻品种构成的自然群体为试验材料,调查了盐、碱胁迫下水稻种子萌发能力相关性状,选择260对SSR标记对基因组进行扫描,采用Structure软件进行群体分析,利用GLM（General Linear Model）方法对标记与幼苗耐盐碱能力进行关联分析;并以试验材料表型均值为对照,鉴别出携带优异等位变异及载体材料。检测到15个与盐胁迫下种子萌发能力关联的SSR位点,其中第10条染色体上分别与标记RM184和RM171连锁位点的贡献率较大,达到29.51%和31.67%,优异等位变异RM184-211表型效应值最大为0.31,载体材料为‘滇屯502选早’。检测到与碱胁迫下种子萌发能力相关联的20个SSR位点,其中第3染色体与RM168和第4染色体与RM6314连锁位点的贡献率较大,分别达到39.17%和50.02%,优异等位变异RM6314-179表型效应值最大为0.58,载体材料为‘越6(N202)’。     

籼稻背景下导入Wx~(in)等位基因改良稻米食味和理化品质

水稻Wx~b等位基因已广泛用于籼稻的品质改良,但携带该等位基因的一些籼稻米饭往往偏软,仍需进一步改良。为明确籼稻背景下导入Wxin等位基因对稻米食味品质和理化品质的效应,分别以携带Wxin的IR64和携带Wx~b的9311为供体,以携带Wxa的籼稻SIR3611 (3611)为受体,基于分子标记辅助选择,通过杂交和连续回交的方式构建了3611背景下携带Wxin和Wx~b的近等基因系。系统比较了不同近等基因系间的农艺性状以及稻米的食味和理化品质。结果表明,近等基因系与受体亲本3611的主要农艺性状基本接近,无显著差异。NIL(Wxin)稻米的表观直链淀粉含量较亲本3611极显著下降而胶稠度极显著增加。NIL(Wx~b)稻米表观直链淀粉含量最低且与之对应的胶稠度最高。近等基因系NIL(Wxin)和NIL(Wx~b)稻米的食味值较亲本极显著提高。NIL(Wx~(in))和NIL(Wx~b)稻米的GBSSI丰度与对应的表观直链淀粉含量具有明显的正相关。稻米粉的黏滞性谱、热糊化特性和晶体结构与直链淀粉含量显著相关性。本研究为在我国籼稻品种品质改良中有效利用Wxin等位基因提供了重要依据。     

Identification of a diverse mini‐core panel of Indian rice germplasm based on genotyping using microsatellite markers

Identification of a small core germplasm set representing the available genetic diversity is essential for its proper evaluation and subsequent utilization in rice improvement programmes. For constituting a small diverse mini‐core panel of Indian rice germplasm, a representative set of 6912 accessions drawn based on their geographic origin from the whole rice germplasm collection available in the National Gene Bank was genotyped using 36 microsatellite markers. Automated fragment analysis of amplicons yielded a total of 435 alleles, with an average 12.4 and range of 3–29 alleles per locus. Polymorphism information content (PIC) ranged from 0.08 (RGNMS190) to 0.86 (RM552) with an average of 0.528. Based on genotyping data, a mini‐core consisting of 98 genotypes was identified. Ninety‐four per cent of the alleles present in the core set were present in the mini‐core. The identified small but diverse panel will be useful for further intensive trait‐specific evaluation and utilization in allele mining.