Technical overview of nuclear microsatellites for Fagus sp., and their utility in F. sylvatica from the central Balkans (Serbia)

ABSTRACT

Selectively neutral nuclear microsatellites (SSRs) are available for Fagus sp., and have been used in F. sylvatica, an ecologically and economically most important European Fagus species. We provide a comprehensive technical overview of available Fagus sp. SSRs (185 loci), carry out meta-analysis of loci used in F. sylvatica (62 loci employed in 62 surveys), and validate a set of 16 loci in 45 individuals of this species from the central Balkans (Serbia). Erroneous usage of marker’s names/authors is rather frequent, and loci successfully used in a number of studies are characterized by other authors by high prevalence of null alleles and even multilocus amplification products. Frequent occurrence of null alleles at FS4-46, used in 26 surveys to date, most likely indicates a failure to record multiple alleles at this locus. Twelve loci are reliable/informative in F. sylvatica from the Balkans (5–18 alleles/locus, H_E ranging from 0.523 to 0.850), while four loci are characterized by high prevalence of null alleles (sfc0161 and sfc1063) and multilocus amplification products (FS4-46 and Fagsyl_007038). Our findings are important for future population genetics and studies on adaptation of F. sylvatica to its environment, because the latter rely on both selectively neutral and adaptive markers under selection.     

Multiple origins for black-grass (Alopecurus myosuroides Huds) target-site-based resistance to herbicides inhibiting acetyl-CoA carboxylase

We have investigated the process of evolution of target-site-based resistance to herbicides inhibiting acetyl-CoA carboxylase (ACCase) in nine French populations of black-grass (Alopecurus myosuroides Huds). To date, two different ACCase resistant alleles are known. One contains an isoleucine-to-leucine substitution at position 1781, the second contains an isoleucine-to-asparagine substitution at position 2041. Using phylogenetic analysis of ACCase sequences, we showed that 1781Leu ACCase alleles evolved from four independent origins in the nine black-grass populations studied, while 2041Asn ACCase alleles evolved from six independent origins. No geographical structure of black-grass populations was revealed. This implies that these populations, although geographically distant, are, or have until recently been, connected by gene flows. Comparison of biological data obtained from herbicide sensitivity bioassay and molecular data showed that distinct resistance mechanisms often exist in a single black-grass population. Accumulation of different resistance mechanisms in a single plant was also demonstrated. We conclude that large-scale evolution of resistance to herbicides in black-grass is a complex phenomenon, resulting from the independent selection of various resistance mechanisms in local black-grass populations undergoing contrasted herbicide and agronomical selection pressures, and connected by gene flows whose parameters remain to be determined.     

Genetic structure of a population of Ganoderma boninense on oil palm

Ganoderma boninense (the causal agent of basal stem rot of oil palm in Papua New Guinea) has a tetrapolar mating system with multiple alleles. Investigations into the population structure of G. boninense , using interfertility between isolates as a marker, revealed that the population on oil palm was comprised predominantly of genetically distinct individuals, although a number of isolates were found to share single mating alleles. No direct hereditary relationship was found between isolates on neighbouring or spatially separated diseased palms, indicating that outcrossing had probably occurred over several generations in the founder population prior to colonization of oil palm. In this study, a total of 81 A and 83 B mating type alleles (factors) were detected with 18 allelic repeats at the A locus and 17 at the B locus. Alleles appeared to be randomly dispersed throughout the population in each study block, although there was a significantly ( P  < 0·01) higher proportion of allelic repeats between estates separated by several kilometres compared to within estates. This is the first study on the population structure of this species and confirms that sexual reproduction is a significant component of the epidemiology of this disease.     

Production of all eight genotypes of null alleles at 'waxy' loci in bread wheat, Triticum aestivum L.

Null alleles of the three loci coding for ‘waxy’ proteins in bread wheat have been identified. Plants carrying different null alleles were collected and segregation of the null alleles in both selfed and doubled haploid progeny of plants simultaneously heterozygous for the null alleles at each of the three loci were examined by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). Mendelian segregation of these alleles in both types of progeny was shown, indicating that they can easily be utilized in breeding programmes. Iodine staining of the eight possible null phenotypes showed that only the triple null type had zero amylose in its endosperm starch.     

芥黄蜜环菌交配型复等位基因的研究

从大兴安岭长白山采集１７号芥黄蜜环菌,用分离的单孢菌株进行交配型测定,证实中国该种为双因子异宗配合机制,选取各号标本的４种交配型菌株进行循环配对实验,结果发现该种的交配型基因座的多样性很高,共有１３对复等位基因,证明该种在世界分布区域内具有较强的生态适应能力。是目前国际首次用实验测定的蜜环菌交配基因数目。     

大豆品种资源抗灰斑病7号生理小种优异等位变异的发掘

本文旨在发掘大豆品种资源中抗灰斑病7号生理小种优异等位变异,为培育抗灰斑病品种提供遗传信息和载体材料。以202份大豆品种为试验材料,鉴定材料抗灰斑病7号生理小种的抗病性。利用SSR标记进行全基因组扫描,采用TASSEL 3.0软件的GLM模型和MLM模型对大豆品种的灰斑病抗性与标记进行关联分析。结果表明,2种模型共同检测到12个与灰斑病7号生理小种抗性显著关联的位点,各标记对表型变异的解释率为2.00%~15.47%,共同检测到增效作用的等位变异共有20个,其中增效表型效应值最大的等位变异是Satt549-263(18.88),载体材料为‘合丰29’;其次为Satt372-291(17.92),载体材料为‘合丰34’。发掘到的等位变异信息和载体材料为培育抗灰斑病品种亲本选配和后代等位条带辅助选择提供了依据。     

籼型矮秆陆稻株高遗传研究

对云南陆稻矮秆×高秆和矮秆×矮秆的株高遗传研究表明，高秆对矮秆均为部分显性，ＩＲ３０７１６—Ｂ—１—８—１—２的矮生性为两对互补隐性主基因控制。其中，１对复等位且显性于ｓｄ—１，暂定为ｓｄ—１＿（ｘ１）。ＣＩＣＡ６为１对隐性主基因控制，可能等位于ｓｄ—１：ＣＩＣＡ９，Ｔ＿（ｏｓ）４０２０，旱谷—２为微效多基因控制，且均具有较强的基因互作。矮化效果，除ＩＲ３０７１６—Ｂ—１—日—１—２外均较好，且遗传力在８５％以上，基因型、表型变异系数很接近，矮化作用能稳定遗传，早代选择效果较好。籼型陆稻矮生基因较水稻丰富、复杂，若将陆稻矮生基因导入水稻，有可能解决水稻株高遗传的单一性和脆弱性。     

小麦显性矮秆基因复等位多态特性研究

 世界小麦矮化育种主要使用隐性矮源。在普通小麦中发现的显性矮源均因导致植株极度矮化（20~55　cm）而未能在小麦育种中广泛应用。笔者发现,将显性矮源矮变1号（4DS携带Rht10,25~30 cm）及矮苏3（4BS携带Rht3,55 cm）的原种大群体种植或施以诱变因子并将其与中、高秆的小麦品种杂交、回交,从其分离世代的大群体中,均可选择到一些株高呈不同程度提升的稳定的突变株系。采用近等基因系法对不同株高突变衍生系的研究表明：其提升的株高真实遗传,各自均携带一个不同株高的半显性矮秆基因,随突变衍生系株高的提升,近等基因系的产量性状显著优化。采用标志基因测交法以及生理生化遗传标记对突变衍生系携带的不同株高的半显性矮秆基因重新进行了基因定位,确认它们分别与Rht10及Rht3的座位相同,因而均是其突变衍生的复等位基因。提出显性矮秆基因具有"复等位多态特性",即极度矮化的显性矮秆基因容易突变为一群株高提高程度不同的、可以达到小麦育种理想株高的半显性矮秆复等位基因。     

水稻显性核不育及其恢复性的遗传规律研究

 对萍乡显性核不育水稻的遗传规律进行了研究,结果表明该不育材料的育性是由两对显性核基因Ms和Rf互作控制的。其中Ms是显性不育基因,Rf是显性上位基因。两者共同存在时,显性上位基因能抑制显性不育基因的表达,从而使育性表现可育。其不育群体的遗传组成为Msmsrfrf+msmsrfrf或MsMsrfrf+MsMsRfRf,恢复系基因型为msmsRfRf。     

Development and evaluation of microsatellite markers for identification of individual Greenshell™ mussels (Perna canaliculus) in a selective breeding programme

A set of 49 microsatellite loci isolated from the endemic New Zealand Greenshell™ mussel, Perna canaliculus, were evaluated for inclusion in a parentage assignment marker suite by assessing their ease of PCR amplification, allele scoring and conformity to Mendelian inheritance in hatchery-produced families. Ten polymorphic loci (mean H_e = 0.78 and polymorphic information content (PIC) = 0.72) were identified as being suitable for parentage assignment. These 10 microsatellite loci gave a combined non-exclusion probability of < 0.001 (probability that an unrelated parent pair will not be excluded from parentage of an arbitrary offspring), based on allele frequencies from 16 broodstock mussels. Simulations predicted an assignment success rate of 99.9% with all 10 loci and > 95% with the best 5 or more loci (mean PIC = 0.84). In actual parentage assignments, 124 offspring from 8 full-sib families were assigned to the correct parent pair with 4 or more loci. We found evidence for null alleles and extensive size homoplasy in many loci, highlighting the importance of thoroughly characterizing and evaluating microsatellite markers prior to parentage assignment and other applications.