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PubMed2005

Selection in backcross programmes.

Backcrossing is a well-known and long established breeding scheme where a characteristic is introgressed from a donor parent into the genomic background of a recurrent parent. The various uses of backcrossing in modern genetics, particularly with the help of molecular markers, are reviewed here. Selection in backcross programmes is used to either improve the genetic value of plant and animal populations or fine map quantitative trait loci. Both cases are helpful in our understanding of the genetic bases of quantitative traits variation.

Animals↗
PubMed1995

A polymorphism in randomly amplified DNA that differentiates the Y chromosomes of Bos indicus and Bos taurus.

A small number of west African Bos taurus cattle breeds, including the N'Dama, constitute a valuable genetic resource by virtue of their ability to remain productive under trypanosomiasis challenge. However, introgression of Bos indicus genes into the trypanotolerant breeds, particularly by introduction of zebu bulls, is a threat to this resource. This work describes the characterization and cloning of a bovine randomly amplified polymorphic DNA (RAPD) that is generated in polymorphic DNA (RAPD) that is generated in polymerase chain reaction (PCR) with the 10 base primer ILO1065 from Bos indicus male templates, but not from B. taurus male templates or female templates of either type. Male-specific sequences with homology to the RAPD also occur in B. taurus breeds. This suggests that the polymorphism may be due to base substitution(s) in an ILO1065 priming site, or insertion/deletion events either affecting priming sites or occurring between sites on the cattle Y chromosome. We have shown that cattle, whether of B. indicus or B. taurus phenotype, which possess a typically B. indicus metaphase Y chromosome on the basis of QFQ banding, have a B. indicus ILO1065-generated genotype. The ILO1065-primed RAPD can be used in a simple dot blot assay as a probe of RAPD-PCR products, to provide a convenient, reliable and effective means of detecting introgression of zebu genes in B. taurus cattle populations.

Africa, Western↗
PubMed2004

Marker-assisted introgression of the Compact mutant myostatin allele MstnCmpt-dl1Abc into a mouse line with extreme growth effects on body composition and muscularity.

Myostatin is a negative regulator of muscle growth and mutations in its gene lead to muscular hypertrophy and reduced fat. In cattle, this is seen in 'double muscled' breeds. We have used marker-assisted introgression to introduce a murine myostatin mutation, MstnCmpt-dl1Abc [Compact (C)], into an inbred line of mice (DUHi) that had been selected on body weight and had exceptional growth. Compared with homozygous wild-type mice, homozygous (C/C) mice of this line were approximately 4-5 % lighter, had approximately 7-8 % shorter tails, substantially increased muscle weights (e.g. quadriceps muscle in males was 59 % heavier) and an increased 'dressing percentage' (approximately 49 % vs 39 %), an indicator of overall muscularity. The weights of several organs (e.g. liver, kidney, heart and digestive tract) were significantly reduced, by 12-20 %. Myostatin deficiency also resulted in drastic reductions of total body fat and of various fat depots, total body fat proportion falling from approximately 17.5 % in wild-type animals of both sexes to 9.5 % and 11.6% in homozygous (C/C) females and males, respectively. Males with a deficiency in myostatin had higher gains in muscle traits than females. Additionally, there was a strong distortion of the segregation ratio on the DUHi background. Of 838 genotyped pups from inter se matings 29 %, 63 % and 8 % were homozygous wild type (+/+), heterozygous (C/+) and homozygous (C/C), respectively, showing that MstnCmpt-dl1Abc has lower fitness on this background. This line, when congenic, will be a useful resource in gene expression studies and for finding modifying genes.

Alleles↗
PubMed2003

Using molecular markers to assess the effect of introgression on quantitative attributes of common bean in the Andean gene pool.

Progress in bean breeding programs requires the exploitation of genetic variation that is present among races or through introgression across gene pools of Phaseolus vulgaris L. Of the two major common bean gene pools, the Andean gene pool seems to have a narrow genetic base, with about 10% of the accessions in the CIAT core collection presenting evidence of introgression. The objective of this study was to quantify the degree of spontaneous introgression in a sample of common bean landraces from the Andean gene pool. The effects of introgression on morphological, economic and nutritional attributes were also investigated. Homogeneity analysis was performed on molecular marker data from 426 Andean-type accessions from the primary centres of origin of the CIAT common bean core collection and two check varieties. Quantitative attribute diversity for 15 traits was studied based on the groups found from the cluster analysis of marker prevalence indices computed for each accession. The two-group summary consisted of one group of 58 accessions (14%) with low prevalence indices and another group of 370 accessions (86%) with high prevalence indices. The smaller group occupied the outlying area of points displayed from homogeneity analysis, yet their geographic origin was widely distributed over the Andean region. This group was regarded as introgressed, since its accessions displayed traits that are associated with the Middle American gene pool: high resistance to Andean disease isolates but low resistance to Middle American disease isolates, low seed weight and high scores for all nutrient elements. Genotypes generated by spontaneous introgression can be helpful for breeders to overcome the difficulties in transferring traits between gene pools.

Breeding↗
PubMed2005

Genetic analysis and conservation of the endangered Canary Island woody sow-thistle, Sonchus gandogeri (Asteraceae).

Sonchus gandogeri, a woody sow-thistle, is an endangered Canary Island endemic with only two known populations, one in the El Golfo and another in the Las Esperillas of El Hierro. Amplified fragment length polymorphism (AFLP) markers were used to assess the genetic variation within and among populations. The mean genetic diversity of two populations was estimated to be 0.380, and the El Golfo population (0.380) had higher genetic diversity than the southeastern one (0.268). The unbiased Nei's genetic identity between the two populations was 0.846. The mean genetic diversity of S. gandogeri was much higher than that of the other endangered plant species. This is perhaps due to breeding system, life form, extinction, and/or introgressive hybridization and hybrid origin of the taxon. This study also indicates that the two populations are not strongly differentiated (G(ST)=0.149). This study suggests that S. gandogeri is more likely to become extinct due to environmental or demographic forces than genetic factors, such as inbreeding depression. More strict control of introduced herbivores is necessary to protect these populations, and germplasm collection for ex situ conservation is needed.

Atlantic Islands↗
PubMed1999

Mitochondrial sequence variation suggests an African influence in Portuguese cattle.

A total of 49 samples from indigenous Portuguese cattle breeds were analysed for sequence variation in the hypervariable region of the mitochondrial DNA D-loop. Sequence comparison and phylogenetic analyses revealed that haplotypes fell into two distinct groups. These corresponded with two separate haplotype clusters into which, respectively, all African, or alternatively all sequences of European origin, have previously been shown to fall. Here, the majority of sequences of African type were encountered in three southern, as compared to three northern breeds. This pattern of African influence may reflect an intercontinental admixture in the initial origins of Iberian breeds, or it is perhaps an introgression dating from the long and influential Moorish occupation of the south of the Iberian peninsula.

Africa↗
PubMed2004

Nucleotide diversity on the ovine Y chromosome.

To investigate the impact of male-mediated introgression during the evolution of sheep breeds, a sequencing approach was used to identify single nucleotide polymorphisms (SNPs) from the male-specific region of the ovine Y chromosome (MSY). A total of 4380 bp, which comprised nine fragments from five MSY genes was sequenced within a panel of 14 males from seven breeds. Sequence alignment identified a single segregating site, an A/G SNP located approximately 1685 bp upstream of the ovine SRY gene. The resulting estimation of nucleotide diversity (piY = 0.90 +/- 0.50 x 10(-4)) falls towards the lower end of estimates from other species. This was compared with the nucleotide diversity estimated from the autosomal component of the genome. Sequence analysis of 2933 bp amplified from eight autosomal genes revealed a nucleotide diversity (piA = 2.15 +/- 0.27 x 10(-3)) higher than previously reported for sheep. Following adjustment for the contrasting influence of effective population size and a male biased mutation rate, comparison revealed that approximately 10% of the expected nucleotide diversity is present on the ovine Y chromosome.

Animals↗
PubMed2003

Fine mapping of quantitative trait loci for improved fruit characteristics from Lycopersicon chmielewskii chromosome 1.

The near-isogenic line (NIL) TA1150 contains a 56-cM introgression from Lycopersicon chmielewskii chromosome 1 and has several interesting phenotypic characteristics including fruit with orange color, high levels of soluble solids, thick pericarp, small stem scars, and good firmness. A set of overlapping recombinant lines (subNILs) was developed and field tested to fine map the quantitative trait loci (QTL) controlling these traits. The results indicated that the solids, pericarp thickness, and firmness QTL are distinct from the color locus. Several of the QTL mapped in this study, including the soluble-solids QTL, probably correspond to QTL mapped in other wild species of tomato. However, analysis of a set of TA523 subNILs containing complementary introgressions from Lycopesicon hirsutum chromosome 1 suggests that this wild species may contain a different locus for improved soluble solids. Thus, it might be possible to combine the L. chmielewskii and L. hirsutum alleles for these loci in a single line with the potential for extremely highly soluble solids. The TA1150 subNIL TA1688 contains the smallest introgression of the solids locus (approximately 19 cM), as well as the pericarp thickness and firmness QTL, with a yield that was equivalent to two of the three control lines. Isolation of recombinant subNILs from TA1688 should break the linkage between orange color and high solids and provide a small introgressed segment for marker-assisted breeding and genetic improvement of processing tomato.

Alleles↗
PubMed2025

Speed breeding: protocols, application and achievements.

One of the limiting factors in breeding and genetic research is the time required to develop pure lines. This is due, on the one hand, to the prolonged vegetative period of a single generation and, on the other hand, to the specifics of inbreeding, which typically requires 4-6 consecutive generations of self-pollination in plant material. Researchers have always sought approaches that enable the rapid development of homozygous plant lines. Consequently, methods such as greenhouse cultivation during the autumn-winter period, single-seed descent, shuttle breeding, embryo culture, and doubled haploid technology have been introduced into practice. All these methods have both advantages and limitations. One of the latest approaches facilitating a significant reduction in the vegetative period of plants is speed breeding (SB). This method is based on the application of factors that shorten the time from sowing to flowering, as well as techniques that accelerate the generative phase of development and overcome postharvest dormancy. This review provides a comprehensive list and characterization of all factors that influence the efficiency of speed breeding to varying degrees. Among the factors discussed that reduce the sowing-to-flowering period are photoperiod, light sources, spectral composition and light intensity, temperature, carbon dioxide levels, vernalization, mineral nutrition, substrate volume, mechanical shoot removal, and the use of plant growth regulators. To shorten the generative phase, the review summarizes the application of embryo culture and forced desiccation of immature seeds, along with methods to overcome postharvest dormancy. Additionally, applications of genetic approaches and genetic engineering for shortening generation time in speed breeding are described. The review also consolidates detailed protocols for approximately thirty crops. The high efficiency of speed breeding in reducing both the vegetative period per generation and the time required to develop pure lines has led to its increasing adoption in various research fields. This review highlights the application of speed breeding for hybridization and pure line development, introgression of target alleles, and genomic selection. A list of phenotypic traits exhibiting high correlation between controlled-environment and field conditions is provided.

accelerated flowering↗
PubMed1996

The estrogen receptor locus is associated with a major gene influencing litter size in pigs.

Identification of individual major genes affecting quantitative traits in livestock species has been limited to date. By using a candidate gene approach and a divergent breed cross involving the Chinese Meishan pig, we have shown that a specific allele of the estrogen receptor (ER) locus is associated with increased litter size. Female pigs from synthetic lines with a 50% Meishan background that were homozygous for this beneficial allele produced 2.3 more pigs in first parities and 1.5 more pigs averaged over all parities than females from the same synthetic lines and homozygous for the undesirable allele. This beneficial ER allele was also found in pigs with Large White breed ancestory. Analysis of females with Large White breed background showed an advantage for females homozygous for the beneficial allele as compared to females homozygous for the other allele of more than 1 total pig born. Analyses of growth performance test records detected no significant unfavorable associations of the beneficial allele with growth and developmental traits. Mapping of the ER gene demonstrated that the closest known genes or markers were 3 centimorgans from ER. To our knowledge, one of these, superoxide dismutase gene (SOD2), was mapped for the first time in the pig. Analysis of ER and these linked markers indicated that ER is the best predictor of litter size differences. Introgression of the beneficial allele into commercial pig breeding lines, in which the allele was not present, and marker-assisted selection for the beneficial allele in lines with Meishan and Large White background have begun.

Animals↗
PubMed2004

Extensive alterations in DNA methylation and transcription in rice caused by introgression from Zizania latifolia.

It has been demonstrated that insertion of foreign DNA into mammalian genome can profoundly alter the patterns of DNA methylation and transcription of the host genome. Introgression of alien DNA into plant genomes through sexual crossing and genetic engineering are commonly used in breeding, but it is not known if plant genomes have similar responses to alien DNA introgression as those of animals. Two stable rice lines with introgression from wild rice, Zizania latifolia, were analyzed for patterns of cytosine DNA methylation and transcription of a set of selected sequences, including cellular genes and transposable element (TE)-related DNA segments. In 21 of the 30 studied sequences, marked changes in DNA methylation and/or transcription were observed compared with those of the rice parent. In all analyzed sequences, the absence of Zizania homologues in the introgression lines was confirmed. No change in DNA methylation and expression patterns was detected in randomly selected individuals of the rice parent nor in two sibling lines without introgressed Zizania DNA. The changed methylation patterns in both introgression lines were stably maintained in all five randomly sampled individuals of a given line, as well as in selfed progenies of the lines. Changed patterns in methylation and expression were also found in an independently produced asymmetric somatic nuclear hybrid (SH6) of rice and Z. latifolia that involves a different rice genotype but also contains a small amount of Z. latifolia DNA integrated into the rice genome. Thus, we have demonstrated that alien DNA introgression into a plant genome can induce extensive alterations in DNA methylation and transcription of both cellular genes and TE-related DNA segments in a genotype-independent manner.

Blotting, Southern↗
PubMed1999

A microsatellite survey of cattle from a centre of origin: the Near East.

Eight humpless cattle breeds from the Near East, three from Europe, one from West Africa and two zebu breeds from India were screened with 20 microsatellite loci. Breeds from the Near East revealed considerable levels of introgression from zebu cattle, which was apparent most in populations from the East and which declined in populations further West. This nonrandom pattern is suggestive of the introduction of zebu cattle from the East. Notwithstanding the overlay of zebu alleles, it was possible to demonstrate that Near Eastern cattle exhibited significantly higher levels of allelic diversity than breeds from other regions, which is consistent with the view that this region represents a primary domestication centre for Bos taurus cattle. The hypothesis that B. taurus and B. indicus cattle have separate domestic origins is also supported by the survey, a large genetic divergence being apparent between the nonhybrid taurine and zebu groups.

Africa↗
PubMedDate not supplied

Genomic contributions in livestock gene introgression programmes.

The composition of the genome after introgression of a marker gene from a donor to a recipient breed was studied using analytical and simulation methods. Theoretical predictions of proportional genomic contributions, including donor linkage drag, from ancestors used at each generation of crossing after an introgression programme agreed closely with simulated results. The obligate drag, the donor genome surrounding the target locus that cannot be removed by subsequent selection, was also studied. It was shown that the number of backcross generations and the length of the chromosome affected proportional genomic contributions to the carrier chromosomes. Population structure had no significant effect on ancestral contributions and linkage drag but it did have an effect on the obligate drag whereby larger offspring groups resulted in smaller obligate drag. The implications for an introgression programme of the number of backcross generations, the population structure and the carrier chromosome length are discussed. The equations derived describing contributions to the genome from individuals from a given generation provide a framework to predict the genomic composition of a population after the introgression of a favourable donor allele. These ancestral contributions can be assigned a value and therefore allow the prediction of genetic lag.

Animals↗
PubMed2006

Sperm motion characteristics of GarolexMalpura sheep evolved in a semi-arid tropical environment through introgression of FecB gene.

The arid and semi-arid tropical climates of India are endowed with vast diversity of non-prolific sheep breeds. The GarolexMalpura sheep has been evolved in a semi-arid tropical environment by introgression of FecB gene via artificial insemination of Malpura ewes using diluted semen of prolific microsheep Garole and subsequently multiplied by inter se mating among GarolexMalpura halfbreds. The aim of the present study was to identify FecB mutation in sexually mature GarolexMalpura rams by forced RFLP-PCR of BMPR-1B gene and evaluate: (i) semen production and sperm motion characteristics of GM rams and (ii) influence of age and FecB genotype on their semen attributes. Semen was collected during autumn season from 12 donor rams by artificial vagina on 8 occasions at weekly interval. The overall means of traits which did not differed significantly with age or FecB genotyping were volume (0.72 ml), mass motility (4.44), sperm concentration (2721.56 x 10(6)ml(-1)), curvilinear velocity (134.51 microm/s), motility (81.3%), amplitude of lateral head displacement (6.24 microm), beat frequency (44.43 Hz), sperm head elongation (48.9%) and sperm head area (10.01 microm(2)). The FecB genotyping had a significant effect (P<0.05) on percent linearity and rapid motile sperms, which did not vary significantly with age. Although sperm concentration was higher in FecB(BB) and FecB(B+), compared to FecB(++) genotypes but the effect was non-significant. The age and FecB genotyping had significant effects (P<0.05) on straightness, average path velocity, straight-line velocity and percentage of medium or slow motile sperms. It is concluded that GarolexMalpura rams with introgressed FecB gene are capable of producing good quality semen in a semi-arid tropical climate.

Aging↗
PubMed1997

Susceptibility of the Namchi and Kapsiki cattle of Cameroon to trypanosome infection.

Two indigenous Cameroonian taurine cattle breeds (Namchi and Kapsiki) were evaluated for trypanosusceptibility following inoculation with Trypanosoma congolense. The degree of zebu ancestry in the experimental animals was assessed using 6 microsatellite markers which are known to have certain unique alleles which are diagnostic of Bos indicus genetic input. Their response to the infection was compared to that of known trypanotolerant (N'Dama) and trypanosusceptible (Ngaoundere Gudali) cattle. The Namchi and the N'Dama controlled the development and severity of anaemia and parasitaemia better than the Kapsiki and the Gudali. For these parameters, there was no significant difference between the N'Dama and Namachi nor between the Kapsiki and Gudali. Similarly, weight loss showed significant breed variation. The N'Dama lost the least weight and the Kapsiki the most. Zebu introgression in the Namchi was comparable to that in the N'Dama while that of the Kapsiki breed was higher, indicating a high level of cross breeding. From the results, the Namchi are considered trypanotolerant while the Kapsiki are trypanosusceptible. The potential exploitation of the indigenous Namchi cattle is discussed.

Alleles↗
PubMed2026

First genomic insights into the introgression of almond PPV-Marcus resistance into peach.

AIM: Sharka, caused by Plum pox virus (PPV), is one of the most damaging viral diseases of stone fruit crops, with peach among the most susceptible cultivated Prunus species. Almond is a promising source of resistance, but its genetic architecture and expression in a peach genetic background remain largely unknown. This study aimed to construct parental genetic linkage maps and identify genomic regions associated with PPV response in almond &#xd7; peach interspecific populations. METHODS: Progenies derived from the almond cultivars 'Del Cid', 'Garrigues', and 'Mono' were evaluated by RT-PCR after graft inoculation with the PPV-Marcus (PPV-M) strain over consecutive infection cycles. Phenotypic data were summarized for each genotype using best linear unbiased estimates (BLUEs). High-density SNP almond and peach arrays were used to construct parental maps for 'Garrigues' and 'Mono' and perform quantitative trait locus (QTL) analysis. RESULTS: Phenotypic variation was observed among and within families. 'Del Cid'-derived progenies showed the greatest resistance, 'Garrigues'-derived progenies displayed intermediate responses, and 'Mono'-derived progenies showed greater susceptibility and variability. The parental maps covered 546.69 cM in 'Mono' and 521.72 cM in 'Garrigues', with average intervals of 0.61 and 1.26 cM per unique marker position, respectively, and showed strong collinearity with the reference genome. QTL associated with PPV-M response were detected on linkage groups (LG) 1 and 6 in 'Garrigues' and LG2 in 'Mono'. The main QTL in 'Garrigues' peaked near 22.39 Mb on LG1, whereas the 'Mono' QTL was located at 22.27-22.62 Mb on LG2; a weaker QTL was detected near 25.38 Mb on LG6 in 'Garrigues'. The results support a quantitative and genetic-background-dependent architecture of PPV resistance. CONCLUSION: This study provides the first evidence of genomic regions associated with PPV-Marcus response in almond &#xd7; peach populations. The detected QTLs provide an initial basis to support the introgression of almond-derived resistance into peach breeding material.

Prunus↗
PubMed2005

[Grain protein content in wheat: genetics of the character and some predictions for its improvement in common wheat].

The results of studies on genetic control of the grain protein content character in common wheat and the attempts of its improvement using traditional breeding approaches and methods of experimental mutagenesis and introgressive hybridization are presented. The evolution of the views on the genetic structure of the character is considered. Possible explanations are given to the fact that the attempts to significantly improve the character in question in common wheat cultivars have failed in spite of long-term genetic and selection studies. Possible lines of further investigation of genetic control of grain protein content and its increase in common wheat are discussed.

Crops, Agricultural↗
PubMed2003

Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations.

Nucleotide sequences of mitochondrial DNA (mtDNA) cytochrome B gene (1140 bp) and control region (707 bp) were used to determine the phylogenetic relationships among 51 pig samples representing ancient and current varieties of Iberian pigs (26), Spanish wild boars (seven) and other domestic pigs (18) of cosmopolitan (Duroc, Large White, Landrace, Pietrain and Meishan) and local (Spotted Black Jabugo, Basque and Mangalitza) breeds. A neighbour-joining tree constructed from pairwise distances provide evidence of the European origin of both Iberian pigs and Spanish wild boars. The introgression of Asian mtDNA haplotypes in the genetic pool of the Iberian breed seems unlikely. Four estimates of sequence divergence between European and Asian clades were calculated from the two main domains of the D-loop region and the synonymous and nonsynonymous nucleotide substitutions in the cytochrome B gene. The time since the divergence of pig ancestors was estimated at about 600,000 years before present.

Animals↗