菰核基因组SSR引物的开发及其在稻族植物中的通用性检测

利用数据库中已有的部分菰(Zizania latifolia Turcz.)核基因组序列,采用in silico方法开发其SSR引物,并选取我国不同纬度的5个菰野生种群,对合成的64对引物进行筛选。结果显示:64对引物中有15对至少在一个种群中表现出多态性;共发现84个等位基因,每个位点平均有5.6个等位基因。在5个种群中,观察杂合度为0.000~0.941,预期杂合度为0.072~0.625。种群间的基因流(Nm=0.576)水平较低导致了种群间表现出较高的遗传分化(FST=0.432)。进一步对稻族其他物种的通用性检测发现,15个多态位点中,有8个位点在亚洲栽培稻(Oryza sativa L.)中得到扩增,有9个位点在普通野生稻(O.rufipogon Griff.)中得到扩增。     

Abundant genetic diversity of the wild rice Zizania latifolia in central China revealed by microsatellites

Wild rice Zizania latifolia is a perennial emergent aquatic plant widely distributed across China. Wild populations of Z. latifolia are important to aquatic ecosystems and are valuable genetic resources for breeding. However, they have been faced with significant habitat losses in recent decades. For 10 nuclear microsatellites, high levels of genetic diversity (H_E = 0.572–0.636) were found across seven surveyed populations from central China. The main factors responsible for that were its long life history and predominant outcrossing reproductive system. Low genetic differentiation among populations was found based on Wright's F_ST = 0.098. Similarly, AMOVA analysis showed only 7.73% of the total molecular variation was attributed to inter‐population differentiation. The weak population structure of Z. latifolia could be due to high gene flow mediated by water or birds (Nm = 2.30, M = 2.18). Importantly, most populations exhibited mutation‐drift disequilibrium, suggesting a recent population decline. Based on the results, wild populations of Z. latifolia are expected to lose genetic diversity and increase genetic structure in future generations. Therefore, conservation management is urgently needed to maintain the genetic resources of Z. latifolia.     

基于mtDNA-COI基因序列的雷氏按蚊分子群体遗传结构研究

【目的】探讨我国雷氏按蚊Anopheles lesteri的群体差异和分化程度。【方法】采用PCR方法, 从分子水平鉴别了采自我国和韩国的雷氏按蚊共9个群体139个样本, 扩增其线粒体DNA细胞色素氧化酶亚基Ⅰ基因, 并进行序列测定和分析。【结果】本研究共获得49个单倍型, 各单倍型呈高水平的平行演化, 来自云南群体的单倍型显示是扩张的源头。分子变异等级分析(AMOVA)的计算结果显示, 群体内变异占总变异的比例（64.95%）大于群体间（35.05%）, FST值为0.3504, 各群体间出现遗传分化。Mantel检验结果显示基因流水平与地理距离呈负相关关系（R²＝0.1322）, 群体遗传结构符合距离隔离模型。【结论】雷氏按蚊韩国和辽宁群体与其他分布地群体间差异大, 已出现明显分化, 我国其他分布地群体间的遗传差异小。     

Nucleotide Polymorphism in the Adh1 Locus of Pearl Millet (Pennisetum Glaucum) (Poaceae)

We investigated nucleotide polymorphism in the Adh1 locus of pearl millet (Pennisetum glaucum) (Poaceae) by determining the DNA sequence of 20 alleles from 10 individuals. The individuals were sampled from throughout pearl millet's indigenous range and represent both wild and cultivated accessions. Our results indicated that there is little nucleotide polymorphism in the Adh1 locus. Estimates of per site nucleotide polymorphism did not differ significantly between cultivated and wild millet accessions. We compared nucleotide polymorphism in pearl millet Adh1 with nucleotide polymorphism in maize (Zea mays) Adh1 and conclude that the maize Adh1 sample is more polymorphic. Increased polymorphism in maize Adh1 may be attributable, in part, to faster substitution rates in the maize lineage. Analysis suggests that substitution rates in the maize Adh1 lineage are ~1.7 times faster than substitution rates in the millet Adh1 lineage.     

基于粪便DNA 的青海雪豹种群遗传结构初步研究

雪豹是国际关注的全球濒危物种,由于独特的生活习性,其确切分布区、种群数量和遗传结构信息非常有限,基于粪便DNA 分析技术的发展为该物种的研究提供了新的手段。在青海省都兰县宗加乡、诺木红乡和治多县索加乡收集到106 份疑似雪豹粪便样品,成功地扩增了78 份粪便样品的mtDNA Cyt b 基因片段,并进行测序。经过GenBank 数据库的Blastn 比对,确定了21 份为雪豹粪便,其中宗加乡11 份、诺木红乡5 份、索加乡5份。经过Clustal W 和DNASP 软件比对分析,在21 份雪豹粪便DNA 中,共检测出7 个多态性位点,分为4 个单倍型,单倍型多态性(h)为0. 384,核苷酸多态性(π)为0.35% 。三个样地之间的遗传距离为0.002 ～ 0.005,核苷酸差异为0.200 ～1. 273。结果表明了3 个取样区均有雪豹存在,且存在较丰富的遗传多态性,样地间也存在一定的遗传差异。     

Natal dispersal and genetic structure in a population of the European wild rabbit (Oryctolagus cuniculus)

A combination of behavioural observation, DNA fingerprinting, and allozyme analysis were used to examine natal dispersal in a wild rabbit population. Rabbits lived in territorial, warren based social groups. Over a 6-year period, significantly more male than female rabbits moved to a new social group before the start of their first breeding season. This pattern of female philopatry and male dispersal was reflected in the genetic structure of the population. DNA fingerprint band-sharing coefficients were significantly higher for females within the same group than for females between groups, while this was not the case for males. Wrighfs inbreeding coefficients were calculated from fingerprint band-sharing values and compared to those obtained from allozyme data. There was little correlation between the relative magnitudes of the F-statistics calculated using the two techniques for comparisons between different social groups. In contrast, two alternative methods for calculating F_ST from DNA fingerprints gave reasonably concordant values although those based on band-sharing were consistently lower than those calculated by an ‘allele’ frequency approach. A negative F_IS value was obtained from allozyme data. Such excess heterozygosity within social groups is expected even under random mating given the social structure and sex-biased dispersal but it is argued that the possibility of behavioural avoidance of inbreeding should not be discounted in this species. Estimates of genetic differentiation obtained from allozyme and DNA fingerprint data agreed closely with reported estimates for the yellow-bellied marmot, a species with a very similar social structure to the European rabbit.     

Decomposition of aboveground and belowground organs of wild rice (Zizania latifolia): mass loss and nutrient changes

Decomposition of aboveground and belowground organs of the emergent macrophyte Z.latifolia was investigated using a litterbag technique for a period of 359 days in a freshwater marsh in Japan. Aboveground parts were classified into: leaves, sheaths and stems. Belowground parts were classified into: horizontal rhizomes (new rhizome, hard rhizome, soft rhizome) and vertical rhizome (stembase). The decay rate (k) was 0.0036 day⁻¹, 0.0033 day⁻¹ and 0.0021 day⁻¹ for leaves, sheaths and stems, respectively. For belowground parts, the decay rate varied considerably from 0.0018 day⁻¹ to 0.0079 day⁻¹, according to differences in the initial chemical compositions of rhizomes. After 359 days of decay, new rhizomes lost 94% of their original dry mass, compared with a loss of 48–84% for the other rhizomes. There was a significant positive relationship between litter quality and decay rate for horizontal rhizomes. For the new rhizomes, which had an internal nitrogen content of 24.2 mg N g⁻¹ dry mass, the mass loss was 40% higher than that of soft rhizomes, which had an internal N content of 9.8 mg N g⁻¹ dry mass. Over the period of 359 days, the nitrogen concentration in all rhizome types decreased to levels lower than initial values, but the phosphorus concentration remained constant after an initial leaching loss. Most nitrogen and phosphorus were lost during the first 45 days of decay. Changes in carbon to nitrogen (C:N) and carbon to phosphorus (C:P) ratios basically followed inversed trends of the nitrogen and phosphorus concentrations.     

Patterns of genetic diversification within the Adh gene family in the grasses (Poaceae).

We investigated the evolutionary dynamics of the Adh gene family within the grasses (Poaceae), with the goal of using molecular evolutionary tools to understand the process of gene family diversification. We analyzed 21 Adh sequences representing a broad array of grasses. Phylogenetic analyses suggested that Adh duplicated into Adh1 and Adh2 before the radiation of the grasses roughly 65 MYA. Gene structure, including intron length, has varied little over this period. Conservation of intron length prompted investigation into the dynamics of intron evolution, particularly the ability of intron sequences to form secondary structures. Intron sequences did not have an extremely high or low minimum free energy of folding relative to permuted sequences, suggesting that individual Adh introns do not evolve under secondary structural constraints. For coding sequences, the diversification of Adh1 and Adh2 was marked by a shift in third-position G + C content. This shift may reflect differential selection for codon use. Diversification between Adh1 and Adh2 was also typified by a shift in nonsynonymous nucleotide substitution rates, but there was no evidence that relatively fast nonsynonymous nucleotide substitution rates in the Adh2 clade were a product of diversifying selection. Gene conversion may have played a role in retarding diversification of Adh1 and Adh2 in rice, but there is no evidence of gene conversion between paralogs in other taxa. Although the reasons for retention of two functional Adh genes remain obscure, we propose that a shift in gene expression was important for the retention of the two Adh gene copies within the grasses.     

Growth and fitness components of wild x cultivated Sorghum bicolor (Poaceae) hybrids in Nebraska

? Premise of the study: Gene flow from crops to wild relatives has received considerable attention since the advent of genetically modified crops. Numerous researchers have found wild-crop hybrids to be nearly as fit as their wild parents, which suggests that crop genes may persist in wild populations. Components of the ecological fitness of cultivated sorghum, its wild relative, shattercane, and their hybrids have not been studied. ? Methods: To assess the potential for gene introgression into shattercane, we crossed cultivated sorghum to a single inbred shattercane line to produce F(1) hybrids and measured growth and several components of ecological fitness in relation to both parents in Nebraska, USA. ? Key results: Germination of F(1) seeds was similar to that of its shattercane parent except at high temperatures, where it was as sensitive as the sorghum parent. The F(1) grew taller and produced more biomass than either parent, but the F(1) leaf area index was intermediate. Fecundity of the F(1) plant was similar to that of shattercane and much greater than that of cultivated sorghum. ? Conclusions: Considering all data, the ecological fitness of shattercane × cultivated sorghum F(1) hybrids may be equivalent to the wild shattercane parent, which suggests that crop genes that are either neutral or beneficial to shattercane would persist in populations within agroecosystems.     

The genetic diversity and population structure of wild soybean evaluated by chloroplast and nuclear gene sequences

Glycine soja, also called wild soybean, is the wild ancestor of domesticated soybean (Glycine max), and one of the world's major cultivated crops. Wild soybean is a valuable resource for the breeding of cultivated soybean and harbors useful genes or agronomic traits. To use and conserve this valuable resource, we conducted a study to evaluate the genetic diversity and population structure of wild soybean using the sequencing data of two nuclear loci (AF105221 and PhyB) and one chloroplast locus (trnQ-rps16) of more than 600 individuals representing 53 populations throughout the natural distribution range. The results showed that most of the variation was found within the populations and groups, but significant genetic differentiation was also detected among different eco-geographical groups. Correlations between genetic and geographical distance at all the loci were consistent with the isolation by distance gene flow model. G. soja exhibited the highest genetic diversity in middle and downstream of Yangzi River (MDYR) region, followed by North East China (NEC), and was the lowest in North West China (NWC). We concluded that both in situ and ex situ conservation strategies required for wild soybean populations, especially which are native to MDYR and NEC regions.     

Responses of early recruitment processes with rhizome to flooding depth and salinity in Manchurian wild rice (Zizania latifolia)

Aquatic Ecology - Environmental stress, such as intense rainfall, drought and salinization, is predicted to increase not only in intensity, but also in frequency under future climate scenarios....     

Population genetic structure and classification of cultivated and wild pea (Pisum sp.) based on morphological traits and SSR markers

Pea (Pisum sativum L.) is an important legume crop that is widely grown worldwide for human consumption and livestock feed. Despite extensive studies, the population genetic structure and classification of cultivated and wild pea (Pisum sp.) remain controversial. To characterize patterns of genetic and morphological variation and investigate the classification of Pisum, we conducted comprehensive population genetic analyses for 323 accessions from cultivated and wild pea, representing three species of Pisum and utilizing 34 morphological traits and 87 polymorphic simple sequence repeat markers. First, we identified three distinct genetic groups among all samples. Group I was primarily composed of Pisum fulvum, Pisum abyssinicum, and some wild P. sativum accessions, whereas Groups II and III consisted of the two genetic groups under P. sativum that represented different geographic distributions of cultivated pea. Analyses of morphological variation revealed significant differences among the three species. Second, among pea germplasms representing eight taxa of Pisum, P. fulvum and P. abyssinicum possessed unique genetic backgrounds and morphological characteristics, corroborating their independent species status. The intraspecific subdivisions of P. sativum described by some authors were not supported in this study, with the exception of several genotypes of P. sativum subsp. elatius that clustered with P. fulvum and P. abyssinicum. Finally, we confirmed that the Chinese pea germplasm was genetically distinct and could be divided into two genetic groups, each of which included both spring-sowing and autumn-sowing ecotypes. These results provide a robust foundation for understanding pea domestication and the utilization of wild genetic resources of pea.     

Molecular phylogeny of the Pooideae (Poaceae) based on nuclear rDNA (ITS) sequences

Phylogenetic relationships of the Poaceae subfamily, Pooideae, were estimated from the sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The entire ITS region of 25 species belonging to 19 genera representing seven tribes was directly sequenced from polymerase chain reaction (PCR)-amplified DNA fragments. The published sequence of rice, Oryza saliva, was used as the outgroup. Sequences of these taxa were analyzed with maximum parsimony (PAUP) and the neighbor-joining distance method (NJ). Among the tribes, the Stipeae, Meliceae and Brachypodieae, all with small chromosomes and a basic number more than x=7, diverged in succession. The Poeae, Aveneae, Bromeae and Triticeae, with large chromosomes and a basic number of x=7, form a monophyletic clade. The Poeae and Aveneae are the sister group of the Bromeae and Triticeae. On the ITS tree, the Brachypodieae is distantly related to the Triticeae and Bromeae, which differs from the phylogenies based on restriction-site variation of cpDNA and morphological characters. The phylogenetic relationships of the seven pooid tribes inferred from the ITS sequences are highly concordant with the cytogenetic evidence that the reduction in chromosome number and the increase in chromosome size evolved only once in the pooids and pre-dated the divergence of the Poeae, Aveneae, Bromeae and Triticeae.This paper reports factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitableThis paper is a cooperative investigation of USDA-ARS and the Utah Agricultural Experiment Station. Logan, Utah 84322. Journal Paper No. 4581     

A spatial genetic structure and effects of relatedness on mate choice in a wild bird population

Inbreeding depression, as commonly found in natural populations, should favour the evolution of inbreeding avoidance mechanisms. If natal dispersal, the first and probably most effective mechanism, does not lead to a complete separation of males and females from a common origin, a small-scale genetic population structure may result and other mechanisms to avoid inbreeding may exist. We studied the genetic population structure and individual mating patterns in blue tits (Parus caeruleus). The population showed a local genetic structure in two out of four years: genetic relatedness between individuals (estimated from microsatellite markers) decreased with distance. This pattern was mainly caused by immigrants to the study area; these, if paired with fellow immigrants, were more related than expected by chance. Since blue tits did not avoid inbreeding with their social partner, we examined if individuals preferred less related partners at later stages of the mate choice process. We found no evidence that females or males avoided inbreeding through extra-pair copulations or through mate desertion and postbreeding dispersal. Although the small-scale genetic population structure suggests that blue tits could use a simple rule of thumb to select less related mates, females did not generally prefer more distantly breeding extra-pair partners. However, the proportion of young fathered by an extra-pair male in mixed paternity broods depended on the genetic relatedness with the female. This suggests that there is a fertilization bias towards less related copulation partners and that blue tits are able to reduce the costs of inbreeding through a postcopulatory process.     

Relationships betweenOryza species (Poaceae) based on 5S DNA sequences

Relationships between 9Oryza species, covering 6 different genomes, have been studied using hybridization and nucleotide sequence information from the5S Dna locus. Four to five units of the major size class of 5S DNA in each species, 55 units in all, were cloned and sequenced. Both hybridization and sequence data confirmed the basic differences between the A and B, C, D genome species suggested by morphological and cytological data. The 5S DNA units of the A genome species were very similar, as were the ones from the B, C, and D genome-containing species. The 5S DNA ofO. australiensis (E genome) grouped with the B, C, D cluster, while the units ofO. brachyantha (F genome) were quite different and grouped away from all other species. 5S DNA units fromO. minuta, O. latifolia, O. australiensis, andO. brachyantha hybridized strongly, and preferentially, to the genomic DNA from which the units were isolated and hence could be useful as species/genome specific probes. The 5S DNA units fromO. sativa, O. nivara, andO. rufipogon provided A genome-specific probes as they hybridized preferentially to A genome DNA. The units fromO. punctata andO. officinalis displayed weaker preferential hybridization toO. punctata DNA, possibly reflecting their shared genome (C genome).     

Comparative RFLP mapping of an allotetraploid wild rice species (Oryza latifolia) and cultivated rice (O. sativa)

The purpose of this study was to construct a comparative RFLP map of an allotetraploid wild rice species, Oryza latifolia, and to study the relationship between the CCDD genome of O. latifolia and the AA genome of O. sativa. A set of RFLP markers, which had been previously mapped to the AA genome of cultivated rice, were used to construct the comparative map. Fifty-eight F₂ progeny, which were derived from a single F₁ plant, were used for segregation analysis. The comparative RFLP map contains 149 DNA markers, including 145 genomic DNA markers from cultivated rice, 3 cDNA markers from oat, and one known gene (waxy, from maize). Segregation patterns reflected the allotetraploid ancestry of O. latifolia, and the CC and DD genomes were readily distinguished by most probes tested. There is a high degree of conservation between the CCDD genome of O. latifolia and the AA genome of O. sativa based on our data, but some inversions and translocations were noted.