Assessment of cattle genetic introgression into domestic yak populations using mitochondrial and microsatellite DNA markers

Hybridization between yak Poephagus grunniens and taurine Bos taurus or indicine B. indicus cattle has been widely practiced throughout the yak geographical range, and gene flow is expected to have occurred between these species. To assess the impact of cattle admixture on domestic yak, we examined 1076 domestic yak from 29 populations collected in China, Bhutan, Nepal, India, Pakistan, Kyrgyzstan, Mongolia and Russia using mitochondrial DNA and 17 autosomal microsatellite loci. A cattle diagnostic marker-based analysis reveals cattle-specific mtDNA and/or autosomal microsatellite allele introgression in 127 yak individuals from 22 populations. The mean level of cattle admixture across the populations, calculated using allelic information at 17 autosomal microsatellite loci, remains relatively low (mY(cattle) = 2.66 +/- 0.53% and Q(cattle) = 0.69 +/- 2.58%), although it varies a lot across populations as well as among individuals within population. Although the level of cattle admixture shows a clear geographical structure, with higher levels of admixture in the Qinghai-Tibetan Plateau and Mongolian and Russian regions, and lower levels in the Himalayan and Pamir Plateau region, our results indicate that the level of cattle admixture is not significantly correlated with the altitude across geographical regions as well as within geographical region. Although yak-cattle hybridization is primarily driven to produce F-1 hybrids, our results show that the subsequent gene flow between yak and cattle took place and has affected contemporary genetic make-up of domestic yak. To protect yak genetic integrity, hybridization between yak and cattle should be tightly controlled.

Artificial interspecific hybridization between Macrobrachium species

Viable F-1 hybrids were obtained from crosses of female Macrobrachium nipponense and male Macrobrachium hainanense involving spermatophore transfer and artificial insemination. This represents the first successful known case of hybridization of two Macrobrachium species by means of artificial insemination. The hatching rate was over 90%. About 20-60% of newly hatched larvae metamorphosed to postlarvae. The morphological characteristics of the hybrids resembled a combination of features of both parents. Malate dehydrogenase (MDH) and esterase (EST) isozyme electrophoresis indicated parents and F-1 hybrids showed co-dominant expression of the paternal and maternal alleles controlling the isozymes and confirmed the hybridization. (C) 2004 Elsevier B.V. All rights reserved.

Assessment of genetic diversities of selected Laminaria (Laminariales, Phaeophyta) gametophytes by inter-simple sequence repeat analysis

Inter-simple sequence repeat (ISSR) analysis was used to assess genetic diversity among 10 pairs of male and female Laminaria gametophytes. A total of 58 amplification loci was obtained from 10 selected ISSR primers, of which 34 revealed polymorphism among the gametophytes. Genetic distances were calculated with the Dice coefficient ranging from 0.006 to 0.223. A dendrogram based on the unweighted pair-group method arithmetic (UPGMA) average showed that most male and female gametophytes of the same species were clustered together and that 10 pairs of gametophytes were divided into four groups. This was generally consistent with the taxonomic categories. The main group consisted of six pairs of gametophytes, which were selected from Laminaria japonica Aresch. by intensive inbreeding through artificial hybridization. One specific marker was cloned, but was not converted successfully into a sequence characterized amplified region (SCAR) marker. Our results demonstrate the feasibility of applying ISSR markers to evaluate Laminaria germplasm diversities.

Isolation and mapping of telomeric pentanucleotide (TAACC)(n) repeats of the pacific whiteleg shrimp, Penaeus vannamei, using fluorescence in situ hybridization

To develop genetic and physical maps for shrimp, accurate information on the actual number of chromosomes and a large number of genetic markers is needed. Previous reports have shown two different chromosome numbers for the Pacific whiteleg shrimp, Penaeus vannamei, the most important penaeid shrimp species cultured in the Western hemisphere. Preliminary results obtained by direct sequencing of clones from a Sau3A-digested genomic library of P. vannamei ovary identified a large number of (TAACC/GGTTA)-containing SSRs. The objectives of this study were to (1) examine the frequency of (TAACC)(n) repeats in 662 P. vannamei genomic clones that were directly sequenced, and perform homology searches of these clones, (2) confirm the number of chromosomes in testis of P. vannamei, and (3) localize the TAACC repeats in P. vannamei chromosome spreads using fluorescence in situ hybridization (FISH). Results for objective I showed that 395 out of the 662 clones sequenced contained single or multiple SSRs with three or more repeat motifs, 199 of which contained variable tandem repeats of the pentanucleotide (TAACC/GGTTA),, with 3 to 14 copies per sequence. The frequency of (TAACC)n repeats in P. vannamei is 4.68 kb for SSRs with five or more repeat motifs. Sequence comparisons using the BLASTN nonredundant and expressed sequence tag (EST) databases indicated that most of the TAACC-containing clones were similar to either the core pentanucleotide repeat in PVPENTREP locus (GenBank accession no. X82619) or portions of 28S rRNA. Transposable elements (transposase for Tn1000 and reverse transcriptase family members), hypothetical or unnamed protein products, and genes of known function such as 18S and 28S rRNAs, heat shock protein 70, and thrombospondin were identified in non-TAACC-containing clones. For objective 2, the meiotic chromosome number of P. vannamei was confirmed as N = 44. For objective 3, four FISH probes (P1 to P4) containing different numbers of TAACC repeats produced positive signals on telomeres of P. vannamei chromosomes. A few chromosomes had positive signals interstitially. Probe signal strength and chromosome coverage differed in the general order of P1 > P2 > P3 > P4, which correlated with the length of TAACC repeats within the probes: 83, 66, 35, and 30 bp, respectively, suggesting that the TAACC repeats, and not the flanking sequences, produced the TAACC signals at chromosome ends and TAACC is likely the telomere sequence for P. vannamei.

Screening of genes related to ovary development in Chinese shrimp Fenneropenaeus chinensis by suppression subtractive hybridization

The ovary of triploid shrimp Fenneropenaeus chinensis was apparently impaired compared to that of the diploid shrimp at the same age. Therefore triploid shrimp ovary is possible to be taken as a model to understand the mechanism of ovary development of shrimp compared to that of the ovary of diploid shrimp at the same age. In the present study, a suppression subtractive hybridization (SSH) technique was applied to identify differentially expressed genes in the ovary between diploid and triploid shrimp. For the forward library (RNA from the ovary of triploid shrimp as the tester), 54 genes were identified. For the reverse library (RNA from the ovary of diploid shrimp as the tester), 16 genes were identified. The identified genes encoded proteins with multiple functions, including extracellular matrix components, cytoskeleton, cell growth and death, metabolism, genetic information processing, signal transduction/transport or immunity related proteins. Eleven differentially expressed genes were selected to be confirmed in the ovaries of triploid and diploid shrimp by semi-quantitative RT-PCR. Genes encoding spermatogonial stem-cell renewal factor, cytochrome c oxidase subunits I and II, clottable protein, antimicrobial peptide and transposase showed up-regulated expressions in the ovary of triploid shrimp. Genes encoding tubulin, cellular apoptosis susceptibility protein, farnesoic acid O-methyltransferase, thrombospondin and heat shock protein 90 genes showed higher expressions in the ovary of diploid shrimp. The differential expressions of the above genes are suggested to be related to the ovary development of shrimp. It will provide a new clue to uncover the molecular mechanisms underlying the ovarian development in penaeid shrimp. (C) 2010 Elsevier Inc. All rights reserved.

LABORATORY HYBRIDIZATION BETWEEN CRASSOSTREA ARIAKENSIS AND C. SIKAMEA

TO understand possible reproductive interaction between Crassostrea ariakensis (Fujita, 1913) and C. sikamea (Amemiya, 1928), which coexist ill estuaries of China and Japan, we conducted 2 X 2 factorial crosses between the two species. Asymmetry in fertilization success was observed where C. sikamea eggs can be fertilized be C. ariakensis the receprocal cross resulted in no fertilization. Fertilization Success ill C.sikamea female X C. ariakemvis male (SA) crosses was lower than that in the two intraspecific crosses and produced larvae that had similar growth the rate as their maternal species during the first nine days because of maternal effects. After that, genome incompatibility casted negative effects on the growth and survival of the hybrid larvae. Most hybrid larvae died during metamorphosis. but a small number of spat survived. Genetic analysis revealed that the survived SA spat contained DNA from both species and were the hybried. This study demonstrates that hybridization between C. ariakensis and C. sikamea is possible in one direction.

Genetic improvement on Chinese shrimp (Fenneropenaeus chinensis): growth and viability performance in F1 hybrids of different populations

Fenneropenaeus chinensis distributed in the Yellow Sea and Bohai Sea of China and the west coast of the Korean Peninsula. Different geographical populations represent potentially different genetic resources. To learn further the characteristics of different geographical population, crosses among two wild and three farmed populations were produced. The two wild populations were from the Yellow Sea and Bohai Sea (WYP), and the west coast of the Korean Peninsula and coast (WKN). The three farmed populations included the offspring of first generation of wild shrimp from coast in Korea (FKN), the Huang Hai (the Yellow Sea in Chinese) No.1 (HH1), and JK98. The phenotypes growth and survival rates of these populations were compared to confirm the feasibility for crossbreeding. The body length (BL), carapace length (CL), carapace width (CW), height of the second and third abdominal segment (HST), width of the second and third abdominal segment (WST), length of the first abdominal segment (LF), length of the last abdominal segment (LL), live body weight (BW), and survival rate were measured. Different combinations were statistically performed with ANOVA and Duncan's Multiple Range Test. The results show that the survival rate of JK98(a (TM) Euro)xWKN(a (TM),) was the highest, followed by WYP(a (TM) Euro)xWKN(a (TM),), FKN(a (TM) Euro)xWYP(a (TM),), FKN(a (TM) Euro)xHH1(a (TM),) and WYP(a (TM) Euro)xFKN(a (TM),); the body weight of FKN(a (TM) Euro)sxHH1(a (TM),) was the highest, followed by FKN(a (TM) Euro)xWYP(a (TM),), WYP(a (TM) Euro)xWKN(a (TM),), WYP(a (TM) Euro)xFKN(a (TM),) and JK98(a (TM) Euro)xWKN(a (TM),); the total length had the same ranking as the body weight. All growth traits in hybrids JK98(a (TM) Euro)xWKN(a (TM),) were the lowest among all combinations. F1 hybrids had significant difference (P < 0.05) in BL, CL, HST, LL, and BW; and insignificant difference (P > 0.05) in other growth traits and survival rate. The results of Duncan's Multiple Range Test are that BL and CL of JK98(a (TM) Euro)xWKN(a (TM),) were significantly different from the other combinations; HST different from the combination of FKN(a (TM) Euro)xWYP(a (TM),), FKN(a (TM) Euro)xHH1(a (TM),) and WYP(a (TM) Euro)xWKN(a (TM),); and BW different from FKN(a (TM) Euro)xWYP(a (TM),) and FKN(a (TM) Euro)xHH1(a (TM),). As a whole, the results indicate that the FKN(a (TM) Euro)xHH1(a (TM),) was the best combination in all growth traits. Therefore, hybridization can introduce the variation to base populations. The systematic selection program based on additive genetic performance may be more effective than crossbreeding.

Survey of Rough and Fuzzy Hybridization.

P. Lingras and R. Jensen, 'Survey of Rough and Fuzzy Hybridization,' Proceedings of the 16th International Conference on Fuzzy Systems (FUZZ-IEEE'07), pp. 125-130, 2007.

Interstitial insertion of varying amounts of ABL-containing genetic material into chromosome 22 in Ph-negative CML.

We studied the cells from three selected patients with Ph-chromosome-negative chronic myeloid leukemia (CML) by Southern blotting, polymerase chain reaction, and in situ hybridization of informative probes to metaphase chromosomes. All three patients had rearrangement of M-BCR sequences in the BCR gene and expression of one or other of the mRNA species characteristic of Ph-positive CML. Leukemic metaphases studied after trypsin-Giemsa banding were indistinguishable from normal. The ABL probe localized both to chromosome 9 and 22 in each case. A probe containing 3' M-BCR sequences localized only to chromosome 22, and not to chromosome 9 as would be expected in Ph-positive CML. Two new probes that recognize different polymorphic regions distal to the ABL gene on chromosome 9 in normal subjects localized exclusively to chromosome 9 in two patients and to both chromosomes 9 and 22 in one patient. These results show that Ph-negative CML with BCR rearrangement is associated with insertion of a variable quantity of chromosome 9 derived material into chromosome 22q11; there is no evidence for reciprocal translocation of material from chromosome 22 to chromosome 9.

Unidirectional hybridization at a species' range boundary: implications for habitat tracking

Aim Introgressive hybridization between a locally rare species and a more abundant congener can drive population extinction via genetic assimilation, or the replacement of the rare species gene pool with that of the common species. To date, however, few studies have assessed the effects of such processes at the limits of species' distribution ranges. In this study, we have examined the potential for hybridization between range-edge populations of the wintergreen Pyrola minor and sympatric populations of Pyrola grandiflora. Location Qeqertarsuaq, Greenland and Churchill, Manitoba, Canada. Methods Genetic analysis of samples from Greenland and Canada was carried out using a combination of nuclear and chloroplast single nucleotide polymorphisms (SNPs). Results Analysis of nuclear SNPs confirmed hybridization in populations of morphologically intermediate individuals, as well as revealing the existence of cryptic hybrids in ostensibly morphologically pure P. minor populations. Analysis of chloroplast SNPs revealed that this hybridization is unidirectional and suggests that hybrids originate via pollen swamping of P. minor by the more common P. grandiflora. Main conclusions Extensive unidirectional hybridization may lead to the extinction of peripheral populations of P. minor where the two species grow sympatrically. Extinction could occur as a result of genetic assimilation where F1s are fertile, or via the removal of unidirectionally pollinated sterile F1s, or by a combination of these processes. This could compromise the ability of species to respond to climate change via habitat tracking, although the final outcome of these processes may ultimately depend on the rate of global climate change and its effect on the species' distributions. © 2009 Blackwell Publishing Ltd.

The incidences of trisomy 8, trisomy 9 and D20S108 deletion in polycythaemia vera: an analysis of blood granulocytes using interphase fluorescence in situ hybridization:an analysis of blood granulocytes using interphase fluorescence in situ hybridization

We have used interphase fluorescence in situ hybridization (IFISH) to detect trisomy 8, trisomy 9 and 20q deletion in circulating granulocytes from patients with polycythaemia vera (PV). Out of 64 PV patients, 15 (23%) exhibited an abnormality. Two patients had trisomy 9, three had trisomy 8 and 10 patients had hemizygous deletion of D20S108 (a locus in the 20q common deleted region). Aberrant nuclei ranged from 10% to 80% in these 15 cases. There was no correlation between the presence of a marker and sex, age, interval between presentation and IFISH analysis, neutrophil or platelet count or therapy. Conventional marrow cytogenetic karyotype results were available in 23 cases and there was concurrence between these and blood IFISH in 16 cases (13 normal and three with 20q/D20S108 deletion by both methods). Three patients with D20S108 deletion by IFISH were normal by previous marrow cytogenetic testing and four cases with 20q deletion by previous marrow cytogenetics had normal blood granulocytes according to IFISH. Thus, we confirm that trisomies 8 and 9 and deletion of 20q are diagnostically useful markers of PV. IFISH analysis of blood granulocytes is a practical method for detecting these markers, but as an adjunct to, not as a substitute for, conventional marrow cytogenetics.

Species introduction promotes hybridization and introgression in Coregonus: is there sign of selection against hybrids?

Species introductions are considered one of the major drivers of biodiversity loss via ecological interactions and genetic admixture with local fauna. We examined two well-recognized fish species, native whitefish (Coregonus lavaretus) and introduced vendace (Coregonus albula), as well as their morphological hybrids in a single lake to test for selection against hybrids and backcrosses in the wild. A representative random subsample of 693 individuals (27.8%) was taken from the total catch of coregonids. This subsample was examined with the aim to select c. 50 individuals of pure whitefish (n = 52), pure vendace (n = 55) and putative hybrid (n = 19) for genetic analyses. The subsequent microsatellites and mitochondrial (mt) DNA analyses provided compelling evidence of hybridization and introgression. Of the 126 fish examined, four were found to be F-1, 14 backcrosses to whitefish and seven backcrosses to vendace. The estimates of historical gene flow suggested higher rates from introduced vendace into native whitefish than vice versa, whereas estimates of contemporary gene flow were equal. Mitochondrial introgression was skewed, with 18 backcrosses having vendace mtDNA and only three with whitefish mtDNA. Hybrids and backcrosses had intermediate morphology and niche utilization compared with parental species. No evidence of selection against hybrids or backcrosses was apparent, as both hybrid and backcross growth rates and fecundities were high. Hybrids (F-1) were only detected in 2 year-classes, suggesting temporal variability in mating between vendace and whitefish. However, our data show that hybrids reached sexual maturity and reproduced actively, with backcrosses recorded from six consecutive year-classes, whereas no F-2 individuals were found. The results indicate widespread introgression, as 10.8% of coregonids were estimated to be backcrosses.

Cryptic introgression into the Kidney saxifrage (Saxifraga hirsuta) from its more abundant sympatric congener Saxifraga spathularis, and the potential risk of genetic assimilation

Background and Aims: Although hybridization can play a positive role in plant evolution, it has been shown that excessive unidirectional hybridization can result in replacement of a species’ gene pool, and even the extinction ofrare species via genetic assimilation. This study examines levels of introgression between the common Saxifraga spathularis and its rarer congener S. hirsuta, which have been observed to hybridize in the wild where they occursympatrically. 
Methods: Seven species-specific single nucleotide polymorphisms (SNPs) were analysed in 1025 plants representing both species and their hybrid, S. polita, from 29 sites across their ranges in Ireland. In addition, species distributionmodelling was carried out to determine whether the relative abundance of the two parental species is likely to change under future climate scenarios. 
Key Results: Saxifraga spathularis individuals tended to be genetically pure, exhibiting little or no introgression from S. hirsuta, but significant levels of introgression of S. spathularis alleles into S. hirsuta were observed, indicatingthat populations exhibiting S. hirsuta morphology are more like a hybrid swarm, consisting of backcrosses and F2s. Populations of the hybrid, S. polita, were generally comprised of F1s or F2s, with some evidence of backcrossing. Species distribution modelling under projected future climate scenarios indicated an increase in suitable habitats for both parental species.
Conclusions: Levels of introgression observed in this study in both S. spathularis and S. hirsuta would appear to be correlated with the relative abundance of the species. Significant introgression of S. spathularis alleles was detectedin the majority of the S. hirsuta populations analysed and, consequently, ongoing introgression would appear to represent a threat to the genetic integrity of S. hirsuta, particularly in areas where the species exists sympatricallywith its congener and where it is greatly outnumbered.

16q24.1 microdeletion in a premature newborn: Usefulness of array-based comparative genomic hybridization in persistent pulmonary hypertension of the newborn.

OBJECTIVE:: Report of a 16q24.1 deletion in a premature newborn, demonstrating the usefulness of array-based comparative genomic hybridization in persistent pulmonary hypertension of the newborn and multiple congenital malformations. DESIGN:: Descriptive case report. SETTING:: Genetic department and neonatal intensive care unit of a tertiary care children's hospital. INTERVENTIONS:: None. PATIENT:: We report the case of a preterm male infant, born at 26 wks of gestation. A cardiac malformation and bilateral hydronephrosis were diagnosed at 19 wks of gestation. Karyotype analysis was normal, and a 22q11.2 microdeletion was excluded by fluorescence in situ hybridization analysis. A cesarean section was performed due to fetal distress. The patient developed persistent pulmonary hypertension unresponsive to mechanical ventilation and nitric oxide treatment and expired at 16 hrs of life. MEASUREMENTS AND MAIN RESULTS:: An autopsy revealed partial atrioventricular canal malformation and showed bilateral dilation of the renal pelvocaliceal system with bilateral ureteral stenosis and annular pancreas. Array-based comparative genomic hybridization analysis (Agilent oligoNT 44K, Agilent Technologies, Santa Clara, CA) showed an interstitial microdeletion encompassing the forkhead box gene cluster in 16q24.1. Review of the pulmonary microscopic examination showed the characteristic features of alveolar capillary dysplasia with misalignment of pulmonary veins. Some features were less prominent due to the gestational age. CONCLUSIONS:: Our review of the literature shows that alveolar capillary dysplasia with misalignment of pulmonary veins is rare but probably underreported. Prematurity is not a usual presentation, and histologic features are difficult to interpret. In our case, array-based comparative genomic hybridization revealed a 16q24.1 deletion, leading to the final diagnosis of alveolar capillary dysplasia with misalignment of pulmonary veins. It emphasizes the usefulness of array-based comparative genomic hybridization analysis as a diagnostic tool with implications for both prognosis and management decisions in newborns with refractory persistent pulmonary hypertension and multiple congenital malformations.

Testing the effects of genetic crossing distance on embryo survival within a metapopulation of brown trout (Salmo trutta)

Predicting progeny performance from parental genetic divergence can potentially enhance the efficiency of supportive breeding programmes and facilitate risk assessment. Yet, experimental testing of the effects of breeding distance on offspring performance remains rare, especially in wild populations of vertebrates. Recent studies have demonstrated that embryos of salmonid fish are sensitive indicators of additive genetic variance for viability traits. We therefore used gametes of wild brown trout (Salmo trutta) from five genetically distinct populations of a river catchment in Switzerland, and used a full factorial design to produce over 2,000 embryos in 100 different crosses with varying genetic distances (FST range 0.005-0.035). Customized egg capsules allowed recording the survival of individual embryos until hatching under natural field conditions. Our breeding design enabled us to evaluate the role of the environment, of genetic and nongenetic parental contributions, and of interactions between these factors, on embryo viability. We found that embryo survival was strongly affected by maternal environmental (i.e. non-genetic) effects and by the microenvironment, i.e. by the location within the gravel. However, embryo survival was not predicted by population divergence, parental allelic dissimilarity, or heterozygosity, neither in the field nor under laboratory conditions. Our findings suggest that the genetic effects of inter-population hybridization within a genetically differentiated meta-population can be minor in comparison to environmental effects.