Genetic diversity and gene flow among pearl millet crop/weed complex: a case study

Weedy plants with intermediate (domesticated × wild) phenotypes occur in most pearl millet fields in West Africa, even in the absence of wild populations. They are usually found, in high numbers, both inside and outside of drills. Questions pertaining to the evolutionary dynamics of diversity within the pearl millet complex (domesticated–weedy–wild forms) were addressed in this study. The diversity of the different components of this complex sampled in two pearl millet fields in two villages of southwestern Niger was assessed at both molecular (AFLP) and morphological levels. Results show that, in both fields, weedy plants found outside of drills are morphologically distinct from weedy plants found inside drills, despite their close similarity at AFLP markers. The data suggest some introgression from the wild to the weedy population but nevertheless that the gene flow between the parapatric wild and domesticated populations is very low. This challenges the traditional view that regular hybridization between domesticated and wild pearl millets explains the abundance of these weedy plants despite farmers’ seed selection. The level of genetic differentiation between fields from the two villages was low when considering domesticated and weedy plants. This could be explained by high gene flow resulting from substantial seed exchanges between farmers. The fact that it is very difficult for farmers to keep their own selected seeds, and the consequent substantial seed exchanges between them, is probably the main factor accounting for the maintenance and dispersal of weedy pearl millets in the region, even in areas where no wild forms have been observed.C. Mariac and T. Robert contributed equally to the work.     

Anthropogenic effects on population genetics of phytophagous insects associated with domesticated plants

The hypothesis of isolation by distance (IBD) predicts that genetic differentiation between populations increases with geographic distance. However, gene flow is governed by numerous factors and the correlation between genetic differentiation and geographic distance is never simply linear. In this study, we analyze the interaction between the effects of geographic distance and of wild or domesticated status of the host plant on genetic differentiation in the bean beetle Acanthoscelides obvelatus. Geographic distance explained most of the among-population genetic differentiation. However, IBD varied depending on the kind of population pairs for which the correlation between genetic differentiation and geographic distance was examined. Whereas pairs of beetle populations associated with wild beans showed significant IBD (P < 10(-4)), no IBD was found when pairs of beetle populations on domesticated beans were examined (P= 0.2992). This latter result can be explained by long-distance migrations of beetles on domesticated plants resulting from human exchanges of bean seeds. Beetle populations associated with wild beans were also significantly more likely than those on domesticated plants to contain rare alleles. However, at the population level, beetles on cultivated beans were similar in allelic richness to those on wild beans. This similarity in allelic richness combined with differences in other aspects of the genetic diversity (i.e., IBD, allelic diversity) is compatible with strongly contrasting effects of migration and drift. This novel indirect effect of human actions on gene flow of a serious pest of a domesticated plant has important implications for the spread of new adaptations such as resistance to pesticides.     

A standardized method for quantifying unidirectional genetic introgression

Genetic introgression of domesticated to wild conspecifics is of great concern to the genetic integrity and viability of the wild populations. Therefore, we need tools that can be used for monitoring unidirectional gene flow from domesticated to wild populations. A challenge to quantitation of unidirectional gene flow is that both the donor and the recipient population may be genetically substructured and that the subpopulations are subjected to genetic drift and may exchange migrants between one another. We develop a standardized method for quantifying and monitoring domesticated to wild gene flow and demonstrate its usefulness to farm and wild Atlantic salmon as a model species. The challenge of having several wild and farm populations was circumvented by in silico generating one analytical center point for farm and wild salmon, respectively. Distributions for the probability that an individual is wild were generated from individual‐based analyses of observed wild and farm genotypes using STRUCTURE. We show that estimates of proportions of the genome being of domesticated origin in a particular wild population can be obtained without having a historical reference sample for the same population. The main advantages of the method presented are the standardized way in which genetic processes within and between populations are taken into account, and the individual‐based analyses giving estimates for each individual independent of other individuals. The method makes use of established software, and as long as genetic markers showing generic genetic differences between domesticated and wild populations are available, it can be applied to all species with unidirectional gene flow. Results from our method are easy to interpret and understand, and will serve as a powerful tool for management, especially because there is no need for a specific historical wild reference sample.     

Allozyme variation in domesticated annual sunflower and its wild relatives

 The annual sunflower (Helianthus annuus L.) is a morphologically and genetically variable species composed of wild, weedy, and domesticated forms that are used for ornament, oilseed, and edible seeds. In this study, we evaluated genetic variation in 146 germplasm accessions of wild and domesticated sunflowers using allozyme analysis. Results from this survey showed that wild sunflower exhibits geographically structured genetic variation, as samples from the Great Plains region of the central United States were genetically divergent from accessions from California and the southwestern United States. Sunflower populations from the Great Plains harbored greater allelic diversity than did wild sunflower from the western United States. Comparison of genetic variability in wild and domesticated sunflower by principal coordinate analysis showed these groups to be genetically divergent, in large part due to differences in the frequency of common alleles. Neighbor-Joining analyses of domesticated H. annuus, wild H. annuus and two closely related wild species (H. argophyllus T. & G. and H. petiolaris Nutt.) showed that domesticated sunflowers form a genetically coherent group and that wild sunflowers from the Great Plains may include the most likely progenitor of domesticated sunflowers. Received: 2 December 1996/Accepted: 4 April 1997     

Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae)

Domesticated materials with well-known wild relatives provide an experimental system to reveal how human selection during cultivation affects genetic composition and adaptation to novel environments. In this paper, our goal was to elucidate how two geographically distinct domestication events modified the structure and level of genetic diversity in common bean. Specifically, we analyzed the genome-wide genetic composition at 26, mostly unlinked microsatellite loci in 349 accessions of wild and domesticated common bean from the Andean and Mesoamerican gene pools. Using a model-based approach, implemented in the software STRUCTURE, we identified nine wild or domesticated populations in common bean, including four of Andean and four of Mesoamerican origins. The ninth population was the putative wild ancestor of the species, which was classified as a Mesoamerican population. A neighbor-joining analysis and a principal coordinate analysis confirmed genetic relationships among accessions and populations observed with the STRUCTURE analysis. Geographic and genetic distances in wild populations were congruent with the exception of a few putative hybrids identified in this study, suggesting a predominant effect of isolation by distance. Domesticated common bean populations possessed lower genetic diversity, higher F _ST, and generally higher linkage disequilibrium (LD) than wild populations in both gene pools; their geographic distributions were less correlated with genetic distance, probably reflecting seed-based gene flow after domestication. The LD was reduced when analyzed in separate Andean and Mesoamerican germplasm samples. The Andean domesticated race Nueva Granada had the highest F _ST value and widest geographic distribution compared to other domesticated races, suggesting a very recent origin or a selection event, presumably associated with a determinate growth habit, which predominates in this race. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild�Cweedy�Ccrop complex in a western African region

Gene flow between domesticated plants and their wild relatives is one of the major evolutionary processes acting to shape their structure of genetic diversity. Earlier literature, in the 1970s, reported on the interfertility and the sympatry of wild, weedy and cultivated sorghum belonging to the species Sorghum bicolor in most regions of sub-Saharan Africa. However, only a few recent surveys have addressed the geographical and ecological distribution of sorghum wild relatives and their genetic structure. These features are poorly documented, especially in western Africa, a centre of diversity for this crop. We report here on an exhaustive in situ collection of wild, weedy and cultivated sorghum assembled in Mali and in Guinea. The extent and pattern of genetic diversity were assessed with 15 SSRs within the cultivated pool (455 accessions), the wild pool (91 wild and weedy forms) and between them. F (ST) and R (ST) statistics, distance-based trees, Bayesian clustering methods, as well as isolation by distance models, were used to infer evolutionary relationships within the wild-weedy-crop complex. Firstly, our analyses highlighted a strong racial structure of genetic diversity within cultivated sorghum (F (ST) = 0.40). Secondly, clustering analyses highlighted the introgressed nature of most of the wild and weedy sorghum and grouped them into two eco-geographical groups. Such closeness between wild and crop sorghum could be the result of both sorghum's domestication history and preferential post-domestication crop-to-wild gene flow enhanced by farmers' practices. Finally, isolation by distance analyses showed strong spatial genetic structure within each pool, due to spatially limited dispersal, and suggested consequent gene flow between the wild and the crop pools, also supported by R (ST) analyses. Our findings thus revealed important features for the collection, conservation and biosafety of domesticated and wild sorghum in their centre of diversity.     

Islands and streams: clusters and gene flow in wild barley populations from the Levant

The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter‐mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analysing a collection of 896 wild barley accessions (Barley1K) from Israel and all available Israeli H. vulgare accessions from the Israeli gene bank. We compared the performance of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) marker data genotyped over a core collection in estimating population parameters. Estimates of gene flow rates with SSR markers indicated a high level of introgression from cultivated barley into wild barley. After removing accessions from the wild barley sample that were recently admixed with cultivated barley, the inference of population structure improved significantly. Both SSR and SNP markers showed that the genetic population structure of wild barley in Israel corresponds to the three major ecogeographic regions: the coast, the Mediterranean north and the deserts in the Jordan valley and the South. Gene flow rates were estimated to be higher from north to south than in the opposite direction. As has been observed in other crop species, there is a significant exchange of alleles between the wild species and domesticated varieties that needs to be accounted for in the population genetic analysis of domestication.     

Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild‐to‐weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed‐shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.     

Genetic structure and relationships within and between cultivated and wild sorghum (<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench) in Kenya as revealed by microsatellite markers

Understanding the extent and partitioning of diversity within and among crop landraces and their wild/weedy relatives constitutes the first step in conserving and unlocking their genetic potential. This study aimed to characterize the genetic structure and relationships within and between cultivated and wild sorghum at country scale in Kenya, and to elucidate some of the underlying evolutionary mechanisms. We analyzed at total of 439 individuals comprising 329 cultivated and 110 wild sorghums using 24 microsatellite markers. We observed a total of 295 alleles across all loci and individuals, with 257 different alleles being detected in the cultivated sorghum gene pool and 238 alleles in the wild sorghum gene pool. We found that the wild sorghum gene pool harbored significantly more genetic diversity than its domesticated counterpart, a reflection that domestication of sorghum was accompanied by a genetic bottleneck. Overall, our study found close genetic proximity between cultivated sorghum and its wild progenitor, with the extent of crop-wild divergence varying among cultivation regions. The observed genetic proximity may have arisen primarily due to historical and/or contemporary gene flow between the two congeners, with differences in farmers’ practices explaining inter-regional gene flow differences. This suggests that deployment of transgenic sorghum in Kenya may lead to escape of transgenes into wild-weedy sorghum relatives. In both cultivated and wild sorghum, genetic diversity was found to be structured more along geographical level than agro-climatic level. This indicated that gene flow and genetic drift contributed to shaping the contemporary genetic structure in the two congeners. Spatial autocorrelation analysis revealed a strong spatial genetic structure in both cultivated and wild sorghums at the country scale, which could be explained by medium- to long-distance seed movement.     

The development of SSR markers by a new method in plants and their application to gene flow studies in azuki bean [<Emphasis Type="Italic">Vigna angularis</Emphasis> (Willd.) Ohwi &; Ohashi]

To gain a better understanding of wild and weedy azuki population structures in relation to the cultigens we have developed simple sequence repeat (SSR) markers based on a new methodology for plant material. In the azuki bean genome, the number of (AG)_n and (AC)_n motif loci per haploid genome has been estimated to be 3,500 and 2,100, respectively, indicating that (AG)_n motifs are a rich source of markers. We constructed a (AG)_n-SSR-enriched library in azuki bean in order to obtain a comprehensive range of SSR markers efficiently. The method applied in this study resulted in a 116-fold enrichment over the non-enriched genomic library, with a high percentage (98%) of successful single-locus amplification by the primer pairs designed. Consequently, this method can be applied to construct SSR-enriched libraries suitable for large-scale sequencing. We obtained 255 unique sequences from an (AG)_n-enriched library for azuki bean. Fifty primer pairs were designed and screened against five populations of wild azuki bean. Among these five populations, one population from Bato town, Tochigi prefecture, Japan, showed greater polymorphism using these primers than the others and was therefore chosen for the in-depth study. The genotypes of 20 individuals were investigated using eight of the SSR primers developed. The genetic relationships among individuals revealed a complex spatial pattern of population structure. Although azuki bean is considered to be a predominantly self-pollinating species, 3 of the 20 individuals tested in the population showed heterozygous genotypes, indicating outcrossing. Allele size and DNA sequence in each of the 20 individuals were compared with those of landraces and released cultivars of azuki bean. Plants in part of the population had many alleles of the same size and with the same sequence as those in cultivated azuki bean, suggesting that gene flow from the cultigen to wild plants has occurred in this population. Unintentional transgene escape from azuki could therefore occur when transgenic azuki is grown in areas where its wild and weedy relatives occur. The approach used here could be applied to biosafety monitoring of transgenic azuki bean.Communicated by C. MöllersX.W. Wang and A. Kaga contributed equally to the results presented in this paper.     

Local scale patterns of gene flow and genetic diversity in a crop–wild–weedy complex of sorghum (Sorghum bicolor (L.) Moench) under traditional agricultural field conditions in Kenya

Little information is available on the extent and patterns of gene flow and genetic diversity between cultivated sorghum and its wild related taxa under local agricultural conditions in Africa. As well as expanding knowledge on the evolutionary and domestication processes for sorghum, such information also has importance in biosafety, conservation and breeding programmes. Here, we examined the magnitude and dynamics of crop–wild gene flow and genetic variability in a crop–wild–weedy complex of sorghum under traditional farming in Meru South district, Kenya. We genotyped 110 cultivated sorghum, and 373 wild sorghum individuals using a panel of ten polymorphic microsatellite loci. We combined traditional measures of genetic diversity and differentiation with admixture analysis, population assignment, and analyses of spatial genetic structure to assess the extent and patterns of gene flow and diversity between cultivated and wild sorghum. Our results indicate that gene flow is asymmetric with higher rates from crop to wild forms than vice versa. Surprisingly, our data suggests that the two congeners have retained substantial genetic distinctness in the face of gene flow. Nevertheless, we found no significant differences in genetic diversity measures between them. Our study also did not find evidence of isolation by distance in cultivated or wild sorghum, which suggests that gene dispersal in the two conspecifics is not limited by geographic distance. Overall our study highlights likely escape and dispersal of transgenes within the sorghum crop–wild–weedy complex if genetically engineered varieties were to be introduced in Africa’s traditional farming systems.     

Genetic structure and diversity of wild sorghum populations (<Emphasis Type="Italic">Sorghum</Emphasis> spp.) from different eco-geographical regions of Kenya

Wild sorghums are extremely diverse phenotypically, genetically and geographically. However, there is an apparent lack of knowledge on the genetic structure and diversity of wild sorghum populations within and between various eco-geographical regions. This is a major obstacle to both their effective conservation and potential use in breeding programs. The objective of this study was to assess the genetic diversity and structure of wild sorghum populations across a range of eco-geographical conditions in Kenya. Sixty-two wild sorghum populations collected from the 4 main sorghum growing regions in Kenya were genotyped using 18 simple sequence repeat markers. The study showed that wild sorghum is highly variable with the Coast region displaying the highest diversity. Analysis of molecular variance showed a significant variance component within and among wild sorghum populations within regions. The genetic structure of wild sorghum populations indicated that gene flow is not restricted to populations within the same geographic region. A weak regional differentiation was found among populations, reflecting human intervention in shaping wild sorghum genetic structure through seed-mediated gene flow. The sympatric occurrence of wild and cultivated sorghums coupled with extensive seed-mediated gene flow, suggests a potential crop-to-wild gene flow and vice versa across the regions. Wild sorghum displayed a mixed mating system. The wide range of estimated outcrossing rates indicate that some environmental conditions may exist where self-fertilisation is favoured while others cross-pollination is more advantageous.     

Genetics and evolution of weedy Helianthus annuus populations: adaptation of an agricultural weed

Agricultural weeds are a major cost to economies throughout the world, and have evolved from numerous plant species in many different plant families. Despite their ubiquity, we do not yet know how easily or often weeds evolve from their wild ancestors or the kinds of genes underlying their evolution. Here we report on the evolution of weedy populations of the common sunflower Helianthus annuus. We analysed 106 microsatellites in 48 individuals from each of six wild and four weed populations of the species. The statistical tests lnRV and lnRH were used to test for significant reductions in genetic variability at each locus in weedy populations compared to nearby wild populations. Between 1% and 6% of genes were significant outliers with reduced variation in weedy populations, implying that a small but not insignificant fraction of the genome may be under selection and involved in adaptation of weedy sunflowers. However, there did not appear to be a substantial reduction in variation across the genome, suggesting that effective population sizes have remained very large during the recent evolution of these weedy populations. Additional analyses showed that weedy populations are more closely related to nearby wild populations than to each other, implying that weediness likely evolved multiple times within the species, although a single origin followed by gene flow with local populations cannot be ruled out. Together, our results point to the relative ease with which weedy forms of this species can evolve and persist despite the potentially high levels of geneflow with nearby wild populations.     

A weed-crop complex in sorghum: The dynamics of genetic diversity in a traditional farming system

Despite the major ecological and economic impacts of gene flow between domesticated plants and their wild relatives, many aspects of the process, particularly the relative roles of natural and human selection in facilitating or constraining gene flow, are still poorly understood. We developed a multidisciplinary approach, involving both biologists and social scientists, to investigate the dynamics of genetic diversity of a sorghum weed-crop complex in a village of Duupa farmers in northern Cameroon. Farmers distinguish a gradient from weedy morphotypes (naa baa see, haariya, and genkiya) to domesticated morphotypes; haariya and genkiya have intermediate morphological traits. We investigated the pattern of diversity in this complex using both morphological and genetic data. Our biological results are interpreted in the light of data on farmers' taxonomy and practices such as spatial pattern of planting and plant selection. Both morphological and genetic data are congruent with farmers' taxonomy and confirm the introgressed status of intermediate weedy morphotypes. Farmers actively select against weedy morphotypes, but several practices unconsciously favor gene flow. Furthermore, haariya and genkiya may facilitate introgression between naa baa see and domesticated morphotypes by virtue of their intermediate flowering period and their mode of management by farmers.     

Estimating the long-term effects of stocking domesticated trout into wild brown trout (Salmo trutta) populations: an approach using microsatellite DNA analysis of historical and contemporary samples

Indigenous salmonid fish gene pools are affected by domesticated conspecifics, derived from aquaculture escapes and deliberate releases. Variability was examined at nine microsatellite loci in order to assess the long-term impact of stocking domesticated trout in two brown trout populations. The study was based on analysis of two historical samples (1945-56), represented by old scale collections, and seven contemporary samples (1986-2000). In one population historical and contemporary samples were remarkably genetically similar despite more than a decade of intense stocking. Estimation of admixture proportions showed a small genetic contribution from domesticated trout (approximately 6%), and individual admixture analysis demonstrated a majority of nonadmixed individuals. The expected genetic contribution by domesticated trout was 64%, assessed from the number of stocked trout and assuming equal survival and reproductive performance of wild and domesticated trout. This demonstrates poor performance and low fitness of domesticated trout in the wild. In another population there was a strong genetic contribution from domesticated trout (between 57% and 88% in different samples), both in samples from a broodstock thought to represent the indigenous population and in a sample of wild spawners. Survival of domesticated trout and admixture with indigenous fish in the broodstock and subsequent stocking into the river, combined with a low population size of native trout relative to the number of stocked trout, could explain the observed introgression. Few nonadmixed individuals remained in the introgressed population, and I discuss how individual admixture analysis can be used to identify and conserve nonintrogressed remains of the population.     

Wild to crop introgression and genetic diversity in Lima bean (Phaseolus lunatus L.) in traditional Mayan milpas from Mexico

Despite the evolutionary, ecological and economic importance of introgression between a domesticated species and its wild relatives in centers of diversity and domestication, the role of traditional farmers in this process has received limited attention. In the Yucatan Peninsula, the region of Mexico that has the greatest amount of domesticated varieties of Lima bean, wild populations grow sympatrically with conspecific varieties, allowing the Mayan farmer to act directly on introgressed seed. We used 11 microsatellite loci to assess levels of introgression in three wild-domesticated complexes of Lima bean from the Yucatan Peninsula and analyze its impact on the genetic diversity of this crop. structure and InStruct analyses showed similar results. The Instruct analysis indicated that the complex with the lowest level of introgression was one where the farmer actively selected against wild plants and introgressed seed. In contrast, the complex with the highest level of introgression was one where the farmer has been consciously selecting a weedy morphotype for 15 years and has already incorporated it into his diet. Genetic diversity of the domesticated pool was higher in the complex with the higher level of introgression. This study showed that farmers have an important role in limiting or favoring the wild to crop introgression and influencing the levels of genetic diversity in their domesticated pool. Only when traditional farmers’ knowledge is taken into account can we correctly understand the dynamics, generation and maintenance of genetic diversity of the landraces in the centers of diversity and domestication.     

走出中国：酿酒酵母的起源、驯养与演化

酿酒酵母(Saccharomyces cerevisiae)被广泛应用于酒类酿造和食品发酵等行业,其被人类利用的历史已有近万年。酿酒酵母也是遗传学、分子生物学、基因组学和合成生物学等研究中常用的模式生物。近年来研究者对其自然和驯养种群进行了全球范围的生态学、群体遗传学和群体基因组学等方面的研究,更新了对其生态分布、遗传多样性、自然进化和驯养史以及进化动力等方面的认知。发现酿酒酵母在原始森林等自然环境中普遍存在,并可能偏好阔叶树树干、腐木和周围土壤等生境。中国酿酒酵母的遗传多样性显著高于世界其他地区,该物种最古老的谱系也仅发现于中国,说明中国可能是该物种的起源地。生态适应是塑造该物种群体结构的主要力量,导致其野生和驯养群体之间的明显分化。驯养群体又分化为固态发酵和液态发酵两大类群,每个类群内又形成不同的驯养谱系。该物种野生群体的遗传多样性远高于其驯养群体,而野生群体遗传多样性的形成主要由中性突变引起。中国野生和驯养群体在麦芽糖利用能力、基因组杂合性、子囊孢子形成率和孢子活力等方面表现出显著差异,表明这2个群体采取不同的生活策略来适应其不同的生活环境。驯养群体通过群体或谱系特异性基因拷贝数...     

Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA

The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing.     

Genetic relationships among domesticated and wild sunflowers (Helianthus annuus,Asteraceae)

Randomly amplified polymorphic DNA (RAPD) loci were used to investigate the origin and genetic relationships of the domesticated sunflower and its wild relatives. A total of 13 primers was employed for the PCR amplifications, from which 68 polymorphic loci were scored. Analysis of RAPD data supports the origin of the domesticated sunflower from wildH. annuus. The high RAPD identity between wild and domesticatedH. annuus (I = 0.976 to I = 0.997) is concordant with a progenitorderivative relationship. However, the identities are very high and therefore provide little information regarding the geographic origin of the domesticated sunflower. Nonetheless, some inferences concerning relationships among domesticated sunflower accessions can be made. The native American varieties and old landracesform a genetically cohesive group based on RAPD evidence, probably due to their origin prior to the use of interspecific hybridization in the development of sunflower cultivars. In contrast, the modern cultivars are not genetically cohesive, perhaps due to the extensive use of intraspecific and interspecific hybridization in the development of modern sunflower varieties. Likewise, little concordance was observed between the geographical origin and genetic clustering of wild populations—an observation probably best explained by the weedy, human dispersed nature of wildH. annuus populations. The information presented here may be a reliable indicator of genetic relationships among wild and domesticated sunflower accessions. However, the processes generating the observed relationships are complex, and the occurrence of unexpected groupings or absence of predicted ones will probably remain difficult to understand.     

草鱼野生与选育群体线粒体DNA控制区D-loop遗传变异分析

为探究经过2个选育世代后选育群体遗传多样性和遗传结构的变化, 研究对4个野生群体(邗江、九江、石首和吴江)和2个选育世代(F1和F2)进行了线粒体DNA控制区(D-loop)序列的遗传变异分析。实验结果表明, 4个野生群体在单倍型数目(H)、单倍型多样性(H_d)、核苷酸多样性(π)、平均核苷酸差异数(K)水平上均高于2个选育世代, 在2个选育世代内表现为F1代群体的核苷酸多样性(π)和平均核苷酸差异数(K)大于F2代群体, 但单倍型多样性(H_d)小于F2代群体; 单倍型分析结果表明, 6个群体间无共享单倍型, 4个野生群体间共发现2种共享单倍型(Hap1和Hap3), 石首群体和2个选育世代共享1种单倍型(Hap15); 遗传分化指数(F_st)分析结果表明, 邗江、九江、吴江3个野生群体和2个选育世代间存在较大的遗传分化(F_st范围为0.41475—0.55128), 石首群体与F1代群体之间存在较小的遗传分化, 与F2代群体之间存在中等水平的遗传分化, 同时F1代群体与F2代群体之间存在较小的遗传分化; 基于6个群体276个个体构建的邻接(Neighbor-Joining, NJ)进化树和基于27种单倍型构建的单倍型网络图也得到了相似的结论, 即邗江、九江、吴江3个野生群体和2个选育世代间的亲缘关系较远, 石首群体和2个选育世代两两之间的亲缘关系较近。以上结果表明, 经过2个世代的选择育种, 选育群体的遗传结构已发生了变化, 并且随着选育的进行, 选育世代的遗传多样性下降的较为明显, 这警示着我们在今后的育种工作中应适当改变现有的选育方案, 并实时监测选育群体的遗传多样性, 以便为今后进一步的选育工作打下坚实的基础。