Identifying footprints of selection in stocked brown trout populations: a spatio‐temporal approach

Studies of interactions between farmed and wild salmonid fishes have suggested reduced fitness of farmed strains in the wild, but evidence for selection at the genic level is lacking. We studied three brown trout populations in Denmark which have been significantly admixed with stocked hatchery trout (19–64%), along with two hatchery strains used for stocking. The wild populations were represented by contemporary samples (2000–2006) and two of them by historical samples (1943–1956). We analysed 61 microsatellite loci, nine of which showed putative functional relationships [expressed sequence tag (EST)‐linked or quantitative trait loci]. F_ST‐based outlier tests provided support for diversifying selection at chromosome regions marked by three loci, two anonymous and one EST‐linked. Patterns of differentiation suggested that the loci were candidates for being under diversifying hitch‐hiking selection in hatchery vs. wild environments. Analysis of hatchery strain admixture proportions showed that in one wild population, two of the loci showed significantly lower admixture proportions than the putatively neutral loci, implying contemporary selection against alleles introduced by hatchery strain trout. In the most strongly admixed population, however, there was no evidence for selection, possibly because of immigration by stocked trout overcoming selection against hatchery‐derived alleles or supportive breeding practices allowing hatchery strain trout to escape natural selection. To our knowledge, this is the first study demonstrating footprints of selection in wild salmonid populations subject to spawning intrusion by farmed fish.     

Genetic variation detected with RAPD markers among upland and lowland rice cultivars (Oryza sativa L.)

Genetic variation of nine upland and four lowland rice cultivars (Oryza sativa L.) was investigated at the DNA level using the randomly amplified polymorphic DNA (RAPD) method via the polymerase chain reaction (PCR). Forty-two random primers were used to amplify DNA segments and 260 PCR products were obtained. The results of agarosegel electrophoretic analysis of these PCR products indicated that 208 (80%) were polymorphic. All 42 primers used in this experiment were amplified and typically generated one-to-four major bands. Only two primers showed no polymorphisms. In general, a higher level of polymorphism was found between japonica and indica subspecies while fewer polymorphisms were found between upland and lowland cultivars within the indica subspecies. A dendrogram that shows the genetic distances of 13 rice cultivars was constructed based on their DNA polymorphisms. Classification of rice cultivars based on the results from the RAPD analysis was identical to the previous classification based on isozyme analysis. This study demonstrated that RAPD analysis is a useful tool in determining the genetic relationships among rice cultivars.     

An AFLP-based survey of genetic diversity and relationships of major farmed cultivars and geographically isolated wild populations of <Emphasis Type="Italic">Saccharina japonica</Emphasis> (Phaeophyta) along the northwest coasts of the Pacific

The genetic diversity and relationships of six representative cultivars and six geographically isolated wild populations of Saccharina japonica along the northwest coasts of the Pacific Ocean were investigated using AFLP markers. A total of 547 bands were generated across all samples by ten primer combinations. At the cultivar or population level, the percentage of polymorphic loci (P), gene diversity (H), and Shannon’s information index (I) was highest in Dalian population (P 59.05%; H 0.2057; I 0.3062) and lowest in Lianjiang cultivar (P 9.87%; H 0.0331; I 0.0497). At the species level, P, H, and I were 85.01%, 0.1948, and 0.3096, respectively. Unique bands were detected in all the six wild populations, with Dalian being the most. In comparison, only Yanza cultivar possessed one unique band. The G _ST value was 0.6226 and the gene flow (N _m ) was 0.1515, indicating strong genetic differentiation among cultivars and populations. Two UMPGA dendrograms were constructed based on the Dice similarity coefficients among individuals and on genetic distances among cultivars and populations, which generally revealed three major clades corresponding to three countries. Analysis of molecular variance revealed that a larger proportion (60.21%) of the total genetic variation was attributable to differences among cultivars and populations. The Mantel test suggested that genetic differentiation was positively correlated with geographic distance (r = 0.7962, P = 0.011) in the six wild populations, agreeing with the isolation by distance model. On the whole, low to moderate genetic diversity within cultivars and populations (except Dalian population) and high genetic differentiation among cultivars and populations were detected.     

26个川茶花品种亲缘关系的ISSR分析

采用ISSR分子标记,对重庆南山植物园中26个品种的川茶花古树进行了ISSR遗传多样性分析。选用14条扩增带型清晰且重复性好的引物共获得166条谱带,其中140条呈多态性,多态性比例(PPB)为84.34％。根据Nei-Li遗传相似性系数在0.708处,UPGMA结果将26个品种分为5个类群,在0.726处可进一步分为10个亚类群;26个川茶花品种的遗传相似性系数介于0.615和0.913之间,平均值为0.704,表明品种间亲缘关系较近。其中牡丹茶与花牡丹之间遗传相似性系数最大,为0.913,表明牡丹茶可能为花牡丹的芽变品种。川渝地区山茶古树资源丰富,但在古树的保护上也面临诸多问题,建议采取相应的措施加以保护。     

Molecular Population Genetics of Rice Domestication

Domestication is a selection process that genetically modifies species to meet human needs. A most intriguing feature of domestication is the extreme phenotypic diversification among breeds. What could be the ultimate source of such genetic variations? Another notable outcome of artificial selection is the reduction in the fitness of domesticated species when they live in the wild without human assistance. The complete sequences of the two subspecies of rice cultivars provide an opportunity to address these questions. Between the two subspecies, we found much higher rates of non‐synonymous (N) than synonymous (S) substitutions and the N/S ratios are higher between cultivars than between wild species. Most interestingly, substitutions of highly dissimilar amino acids that are deleterious and uncommon between natural species are disproportionately common between the two subspecies of rice. We suggest strong selection in the absence of effective recombination may be the driving force, which we called the domestication‐associated Hill‐Robertson effect. These hitchhiking mutations may contribute to some fitness reduction in cultivars. Comparisons of the two genomes also reveal the existence of highly divergent regions in the genomes. Haplotypes in these regions often form highly polymorphic linkage blocks that are much older than speciation between wild species. Genes from such regions could contribute to the differences between indica and japonica and are likely to be involved in the diversifying selection under domestication. Their existence suggests that the amount of genetic variation within the single progenitor species Oryza rufipogon may be insufficient to account for the variation among rice cultivars, which may come from a more inclusive gene pool comprising most of the A‐genome wild species. Genes from the highly polymorphic regions also provide strong support for the independent domestication of the two subspecies. The genomic variation in rice has revealing implications for studying the genetic basis of indica‐japonica differentiation under rice domestication and subsequent improvement.     

Testing and validating a modified CTAB DNA extraction method to enable molecular parentage analysis of fertilized eggs and larvae of an emerging South African aquaculture species,the dusky kob Argyrosomus japonicus

This study describes the successful implementation of a modified cetyltrimethyl ammonium bromide (CTAB) protocol to isolate genomic DNA and amplify 14 microsatellite markers from fertilized eggs and larvae of an emerging South African farmed marine fish species, the dusky kob Argyrosomus japonicus. To test and validate the efficiency of this method, genetic data were utilized to resolve parentage and kinship of first‐generation (F1) offspring produced in mass‐spawning events of wild broodstock fish in a commercial hatchery.     

Genetic monitoring of the Amazonian fish matrinchã (Brycon cephalus) using RAPD markers: insights into supportive breeding and conservation programmes

The importance of genetic evaluations in aquaculture programmes has been increased significantly not only to improve effectiveness of hatchery production but also to maintain genetic diversity. In the present study, wild and captive populations of a commercially important neotropical freshwater fish, Brycon cephalus (Amazonian matrinchã), were analyzed in order to evaluate the levels of genetic diversity in a breeding programme at a Brazilian research institute of tropical fish. Random Amplified Polymorphic DNA fingerprinting was used to access the genetic variability of a wild stock from the Amazon River and of three captive stocks that correspond to consecutive generations from the fishery culture. Although farmed stocks showed considerably lower genetic variation than the wild population, a significantly higher level of polymorphism was detected in the third hatchery generation. The results seem to reflect a common breeding practice on several hatchery fish programmes that use a small number of parents as broodstocks, obtaining reproductive success with few non‐identified mating couples. The obtained data were useful for discussing suitable strategies for the genetic management and biodiversity conservation of this species.     

Influence of immune‐relevant genotype on the reproductive success of a salmonid alternative mating strategy

Major histocompatibility complex (MHC) and immune‐relevant gene markers were used to evaluate differences in reproductive success (RS) among naturally spawning coho salmon Oncorhynchus kisutch mate pairs involving an alternative male reproductive phenotype, known as jacks. These mate pairs included both hatchery‐reared and wild origin fish such that three classes were evaluated in two consecutive years (2005 and 2006) using a previously constructed multigenerational genetic pedigree: wild × wild (W × W), hatchery × hatchery (H × H) and wild × hatchery (W × H). Oncorhynchus kisutch jack mate pairs mated randomly based on immune‐relevant genotype in both years; a result consistent with the opportunistic mating strategy of jacks. An association between greater number of alleles shared at three immune‐relevant gene markers and increased RS was found for: W × H mate pairs in 2005 (BHMS429), W × H pairs in 2006 (SsalR016TKU) and W × W pairs in 2006 (OMM3085). No correlation between immune gene diversity and RS was found for H × H pairs in either year. The results suggest that the influence of immune‐relevant genotype on mating success may be different for jacks when compared with previous studies of large adult male O. kisutch.     

TOND1 confers tolerance to nitrogen deficiency in rice

Nitrogen (N), the most important mineral nutrient for plants, is critical to agricultural production systems. N deficiency severely affects rice growth and decreases rice yields. However, excessive use of N fertilizer has caused severe pollution to agricultural and ecological environments. The necessity of breeding of crops that require lower input of N fertilizer has been recognized. Here we identified a major quantitative trait locus on chromosome 12, Tolerance Of Nitrogen Deficiency 1 (TOND1), that confers tolerance to N deficiency in the indica cultivar Teqing. Sequence verification of 75 indica and 75 japonica cultivars from 18 countries and regions demonstrated that only 27.3% of cultivars (41 indica cultivars) contain TOND1, whereas 72.7% of cultivars, including the remaining 34 indica cultivars and all 75 japonica cultivars, do not harbor the TOND1 allele. Over‐expression of TOND1 increased the tolerance to N deficiency in the TOND1‐deficient rice cultivars. The identification of TOND1 provides a molecular basis for breeding rice varieties with improved grain yield despite decreased input of N fertilizers.     

29个香蕉基因型遗传多样性的SRAP分析

采用SRAP分子标记技术对29个香蕉品种(系)的多样性进行研究,结果显示,64对SRAP引物中筛选出25个多态性较高的引物组合,共扩增出324条条带;UPGAM聚类图显示所有供试的29个香蕉品种(系)可分为2个类群且与基因型相一致;实验结果与形态、农艺性状标记分类基本一致。研究表明,SRAP技术可有效运用于香蕉基因型的遗传和育种研究。     

Better performance of germination in hyperosmotic solutions in conspecific weedy rice than cultivated rice

Weeds and crops that grow together often confront similar types of environmental stress, especially drought stress. Weedy rice (Oryza sativa f. spontanea) and cultivated rice (O. sativa L.) provide a unique pair consisting of a weed and a conspecific model crop that can be used to study the drought tolerance of plants across a large distributional range. The investigation on weedy rice's damage to paddy fields showed that it was more serious in dry direct seeding than water direct seeding. Compared with water direct seeding, the seeds of cultivated rice and weedy rice in dry direct seeding will absorb water and germinate under the condition of insufficient soil moisture. Our hypothesis is that weedy rice seeds have evolved stronger germination ability than coexisting cultivated rice under water stress, so that they can obtain more growth space in the early stage in dry direct seeding and thus obtain higher fitness. Seeds of weedy rice populations and coexisting rice cultivars were collected from 61 sites across China and were germinated with 20% polyethylene glycol‐6000 to simulate drought stress. Two drought response indices, which assessed germination rate and germination index, plus one germination stress tolerance index, indicated significantly greater drought tolerance in weedy rice populations than in coexisting rice cultivars (P < 0.01). Drought tolerance for the three indexes were indica weedy rice > indica rice cultivars, japonica weedy rice > japonica rice cultivars, and indica weedy rice > japonica rice cultivars. These results indicate that weedy rice populations show stronger drought stress tolerance than coexisting rice cultivars at various sites, specifically during the seed germination period. Furthermore, Pearson's correlation found that drought response of weedy rice populations and coexisting rice cultivars were significantly different with these environmental factors: latitude, altitude, annual mean precipitation, mean annual temperature, mean precipitation in the sowing month, mean temperature in the sowing month, and sowing methods. Weedy rice shows different patterns of drought tolerance variation across geographical (latitude and altitude) and environmental (precipitation) gradients compared to coexisting rice cultivars. This study suggests that weedy rice might have evolved new drought tolerance and could provide a useful source of genetic resources for improving drought tolerance of crop cultivars and breeding direct seeded cultivars to reduce the usage of seeds in direct seeding.     

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm. On the basis of model-based grouping, neighbour-joining tree and principal coordinate analysis, we confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm. With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and showed that Chinese temperate japonica contained higher diversity than that of global samples, whereas Chinese indica and tropical japonica maintained slightly lower diversity than that present in the global samples. Particularly, we observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups of Chinese cultivars, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments.     

Selecting genetic transformants of indica and indica-derived rice cultivars using bispyribac sodium and a mutated ALS gene

Bispyribac sodium (BS), a pyrimidinyl carboxy herbicide, is a well-known inhibitor of acetolactate synthase (ALS) activity. ALS is an enzyme in the biosynthetic pathway for branched-chain amino acids. A mutant form of rice ALS (OsmALS [W548L/S627I]) that confers resistance to BS can be used as an in vitro selection marker gene for plant transformation. Since indica and indica-derived cultivars are thought to have lower BS sensitivity than japonica rice, the application of BS as a selectable reagent for genetic transformation in indica and indica-derived cultivars is more challenging than for japonica cultivars. In this study, callus and seedlings of eight different rice cultivars (five indica-derived cultivars, two indica cultivars and one japonica cultivar) were tested for BS sensitivity. Our study indicates for the first time that callus shows a higher sensitivity to BS than seedlings in indica and indica-derived cultivars. We used BS with OsmALS [W548L/S627I] to select transformed calli, and transgenic rice plants from indica and indica-derived cultivars were successfully obtained.     

Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

Rufiji tilapia (Oreochromis urolepis urolepis) is an endemic cichlid in Tanzania. In addition to its importance for biodiversity conservation, Rufiji tilapia is also attractive for farming due to its high growth rate, salinity tolerance, and the production of all‐male hybrids when crossed with Nile tilapia (Oreochromis niloticus). The aim of the current study was to assess the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations in order to inform conservation and aquaculture practices. Double‐digest restriction‐site‐associated DNA (ddRAD) libraries were constructed from 195 animals originating from eight wild (Nyamisati, Utete, Mansi, Mindu, Wami, Ruaha, Kibasira, and Kilola) and two farmed (Bwawani and Chemchem) populations. The identified single nucleotide polymorphisms (SNPs; n = 2,182) were used to investigate the genetic variation within and among the studied populations. Genetic distance estimates (F_st) were low among populations from neighboring locations, with the exception of Utete and Chemchem populations (F_st = 0.34). Isolation‐by‐distance (IBD) analysis among the wild populations did not detect any significant correlation signal (r = .05; p‐value = .4) between the genetic distance and the sampling (Euclidean distance) locations. Population structure and putative ancestry were further investigated using both Bayesian (Structure) and multivariate approaches (discriminant analysis of principal components). Both analysis indicated the existence of three distinct genetic clusters. Two cross‐validation scenarios were conducted in order to test the efficiency of the SNP dataset for discriminating between farmed and wild animals or predicting the population of origin. Approximately 95% of the test dataset was correctly classified in the first scenario, while in the case of predicting for the population of origin 68% of the test dataset was correctly classified. Overall, our results provide novel insights regarding the population structure of Rufiji tilapia and a new database of informative SNP markers for both conservation management and aquaculture activities.     

25份槭属优良种质资源亲缘关系的ISSR分析

槭属植物是世界园林绿化中的重要植物种类,种质资源丰富且大多数种类具有重要的观赏价值。针对目前我国槭属植物杂交育种工作中面临的品种混杂不清、亲缘状况不明等情况,该研究采用ISSR分子标记对槭属25份植物材料进行了亲缘关系分析。结果表明:选用12条扩增带型清晰且重复性好的引物共获得84条谱带,其中81条呈多态性,多态性比例(PPB)达96.43%,表明槭属植物遗传多样性较高。25份槭属植物材料的遗传相似性系数介于0.405与0.952之间,平均值为0.627,表明不同品种或物种之间遗传相似性系数变化较大。根据Nei遗传相似性系数,在0.578处,UPGMA结果将25份植物材料分为2个类群,其中鸡爪槭品种(或变种)聚为一类,显示了各品种(或变种)之间具有较高的亲缘关系,其余槭属植物则聚为类群II;在0.646处,可进一步分为6个亚类群,部分鸡爪槭品种间表现出了叶形、叶色等表型形状与其遗传关系的相关性。研究未发现鸡爪槭品种(或变种)的亲缘关系与地理分布存在相关性。我国槭树资源丰富,但目前我国对槭树新品种的开发及选育工作仍十分薄弱,建议采取自行选育结合国外引进新品种的方式,丰富我国的槭树种质资源。     

Biochemical Polymorphism in Yellow Catfish, Mystus nemurus (C&V), from Thailand

Yellow catfish, Mystus nemurus (Cuv. & Val.), is becoming one of the major freshwater species farmed by aquaculturists in Southeast Asia. It was of interest to examine levels of genetic subpopulation differentiation among samples of this species obtained from parts of its range, as well as to compare the genetics of wild and hatchery-bred fish. Horizontal starch gel electrophoresis and histochemical staining techniques were used to examine genetic variation within and among eight wild and one hatchery populations of M. nemurus from northern, northeastern, central and southern Thailand. Four tissues (heart, liver, kidney, and muscle) from individual specimens were used to analyze variations at 23 protein-coding loci. Fifteen of the 23 loci examined (65.22%), namely, ACP*, AAT-1*, EST-1*, EST-2*, GPI*, IDH-1*, IDH-2*, MDH-1*, MDH-2*, MDH-3*, ME*, PGM*, 6PGD*, SOD*, and HB*,were polymorphic at the 0.95 level. Observed heterozygosities ranged from 0.041 to 0.111, with an average of 0.068 ± 0.028. Genetic distances ranged from 0.005 to 0.164. The greatest genetic distance was found between the Chainat and the Suratthani populations (0.164), a level indicative of subspecific differentiation in M. nemurus from within Thailand.     

Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP

Gossypium species (± 49) represent a vast resource of genetic diversity for the improvement of cultivated cotton. To determine intra- and inter-specific genetic relationships within a diverse collection of Gossypium taxa, we employed 16 AFLP primer combinations on three diploid species, Gossypium herbaceum L. (A1), Gossypium arboreum L. (A2) and Gossypium raimondii Ulbrich (D5), and 26 AD allotetraploid accessions (Gossypium barbadense L. and Gossypium hirsutum L.). A total of 1180 major AFLP bands were observed; 368 of these (31%) were polymorphic. Genetic similarities among all taxa ranged from 0.21 (between the diploid species G. arboreum and G. raimondii) up to 0.89 (within G. barbadense). Phenetic trees based on genetic similarities (UPGMA, N-J) were consistent with known taxonomic relationships. In some cases, well-supported phylogenetic relationships, as well as evidence of genetic reticulation, could also be inferred. UPGMA trees and principal coordinate analysis based on genetic similarity matrices were used to identify genetically distinct cultivars that are potentially important sources of germplasm for cotton improvement, particularly of fiber quality traits. We show that AFLP is useful for estimating genetic relationships across a wide range of taxonomic levels, and for analyzing the evolutionary and historical development of cotton cultivars at the genomic level. Received: 17 January 2000 / Accepted: 4 May 2000     

Origin of cytoplasm substituted rice cultivars found in Japan

Genetic variation of Japanese rice cultivars were examined. Five of 450 lowland cultivars and another five of 200 upland cultivars were determined as the indica type by using isozyme genotypes and the remainder were of the japonica type. The major characteristics of these indica cultivars, revealed a slender shape of grains, a short apiculus hair length, a positive allele for Ph reaction, and allele-3 for the Pgd1 locus. Three of these indica cultivars showed a non-deletion ORF100, which is essential to the japonica-type plastid. The plastid subtype identity (PS-ID) sequences of these plastids is 6C7A, which is also a japonica-specific repeat unit. Thus, these cultivars were concluded to be naturally generated cytoplasm substituted lines. These plastids were introduced into a indica genetic background from japonica cultivars grown elsewhere. The rest of the indica cultivars revealed a deletion-type ORF100 and plastid subtype 8C8A, both of which are indica-specific. These cultivars carried indica-type allelic constitutions for diagnostic isozyme loci. However, other characters were identical to the cytoplasm-substituted cultivars in Japan. In East and Southeast Asia, cultivars carrying a indica-type nuclear genotype with a japonica-type plastid are restricted to Aus cultivars in the Bengal region. Genetic and historical records suggest that Japanese indica cultivars and the Aus cultivars are closely related. The Aus cultivars acquire necessary genetic constitutions from both indica and japonica cultivars through naturally occurring out-crossing to adapt to a particular cultivation condition in the region. The wide adaptability enabled them to be introduced into a northern region like Japan.     

Single-seeded InDel fingerprints in rice:An effective tool for indica-japonica rice classification and evolutionary studies

Asian cultivated rice(Oryza sativa L.),an important cereal crop worldwide,was domesticated from its wild ancestor 8000 years ago.During its long-term cultivation and evolution under diverse agroecological conditions, Asian cultivated rice has differentiated into indica and japonica subspecies.An effective method is required to identify rice germplasm for its indica and japonica features,which is essential in rice genetic improvements.We developed a protocol that combined DNA extraction from a single rice seed and the insertion/deletion(InDel) molecular fingerprint to determine the indica and japonica features of rice germplasm.We analyzed a set of rice germplasm,including 166 Asian rice varieties,two African rice varieties,30 accessions of wild rice species,and 42 weedy rice accessions,using the single-seeded InDel fingerprints(SSIF).The results show that the SSIF method can efficiently determine the indica and japonica features of the rice germplasm.Further analyses revealed significant indica and japonica differentiation in most Asian rice varieties and weedy rice accessions.In contrast,African rice varieties and nearly all the wild rice accessions did not exhibit such differentiation.The pattern of cultivated and wild rice samples illustrated by the SSIF supports our previous hypothesis that indica and japonica differentiation occurred after rice domestication under different agroecological conditions.In addition,the divergent pattern of rice cultivars and weedy rice accessions suggests the possibility of an endoferal origin(from crop)of the weedy rice included in the present study.