A simplified QTL mapping approach for screening and mapping of novel AFLP markers associated with beef marbling

Identification and characterization of novel single nucleotide polymorphism markers for fat deposition in muscle tissue of pigs using amplified fragment length polymorphism

Objective

This study was conducted to identify and evaluate the effective single nucleotide polymorphism (SNP) markers for fat deposition in the longissimus dorsi muscles of pigs using the amplified fragment length polymorphism (AFLP) approach.

Methods

Sixty-four selective primer combinations were used to identify the AFLP markers in the 20 highest- and 20 lowest-intramuscular fat (IMF) content phenotypes. Five AFLP fragments were converted into simple codominant SNP markers. These SNP markers were tested in terms of their association with IMF content and fatty acid (FA) composition traits in 620 commercially crossbred pigs.

Results

The SSC7 g.4937240C>G marker showed an association with IMF content (p<0.05). The SSC9 g.5496647_5496662insdel marker showed a significant association with IMF content and arachidonic levels (p<0.05). The SSC10 g.71225134G>A marker revealed an association with palmitoleic and ω9 FA levels (p<0.05), while the SSC17 g.61976696G>T marker showed a significant association with IMF content and FA levels of palmitoleic, eicosenoic, arachidonic, monounsaturated fatty acids, and ω9 FA levels. However, no significant association of SSC8 g.47338181G>A was observed with any IMF and FA levels in this study.

Conclusion

Four SNP markers (SSC7 g.4937240C>G, SSC9 g.5496647_5496662insdel, SSC10 g.71225134G>A, and SSC17 g.61976696G>T) were found to be associated with IMF and/or FA content traits in commercially crossbred pigs. These findings provide evidence of the novel SNP markers as being potentially useful for selecting pigs with the desirable IMF content and FA composition.

Identification of Single-Locus PCR-Based Markers Linked to Shell Background Color in the Pacific Oyster (Crassostrea gigas)

A number of Pacific oyster (Crassostrea gigas) with golden shell background color were obtained which show great potential to develop a niche market. To improve the selective breeding progress of true-breeding strains with complete golden oysters, research was conducted to identify genetic markers linked to the shell color locus. An F1-segregating population was obtained by crossing two oysters with golden shell and white shell. Genomic DNA from eight progenies with golden shell and eight progenies with white shell were equally pooled for amplified fragment length polymorphism (AFLP) screening. In bulked segregant analysis, six out of 225 selective primer pair combinations produced seven polymorphic fragments tightly linked to shell color across the segregating population. The seven AFLP markers were all derived from the golden dam and mapped onto a single linkage group flanking the shell color locus. In conversion of the AFLPs into single-locus PCR-based markers, a sequence-characterized amplified region (SCAR) marker, named SCARJ8-2, a single nucleotide polymorphism (SNP) marker, named SNPL2-4, and a simple sequence repeat (SSR) marker, named SSRO11-2, were obtained. These markers obtained in this study will be useful for marker-assisted selection of the Pacific oyster.

High-density genetic maps for loci involved in nuclear male sterility (NMS1) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L., Asteraceae)

High-density genetic maps were constructed for loci involved in nuclear male sterility (NMS1-locus) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L.). The mapping population consisted of 389 F1' individuals derived from a cross between two plants, K28 (male-sterile) and K59 (pollen-fertile), both heterozygous at the S-locus. This F1' mapping population segregated for both male sterility (MS) and strong self-incompatibility (SI) phenotypes. Phenotyping F1' individuals for MS allowed us to map the NMS1-locus to linkage group (LG) 5, while controlled diallel and factorial crosses to identify compatible/incompatible phenotypes mapped the S-locus to LG2. To increase the density of markers around these loci, bulked segregant analysis was used. Bulks and parental plants K28 and K59 were screened using amplified fragment length polymorphism (AFLP) analysis, with a complete set of 256 primer combinations of EcoRI-ANN and MseI-CNN. A total of 31,000 fragments were generated, of which 2,350 showed polymorphism between K59 and K28. Thirteen AFLP markers were identified close to the NMS1-locus and six in the vicinity of the S-locus. From these AFLP markers, eight were transformed into sequence-characterized amplified region (SCAR) markers and of these five showed co-dominant polymorphism. The chromosomal regions containing the NMS1-locus and the S-locus were each confined to a region of 0.8 cM. In addition, we mapped genes encoding proteins similar to S-receptor kinase, the female determinant of sporophytic SI in the Brasicaceae, and also markers in the vicinity of the putative S-locus of sunflower, but none of these genes or markers mapped close to the chicory S-locus.

Database of cattle candidate genes and genetic markers for milk production and mastitis

A cattle database of candidate genes and genetic markers for milk production and mastitis has been developed to provide an integrated research tool incorporating different types of information supporting a genomic approach to study lactation, udder development and health. The database contains 943 genes and genetic markers involved in mammary gland development and function, representing candidates for further functional studies. The candidate loci were drawn on a genetic map to reveal positional overlaps. For identification of candidate loci, data from seven different research approaches were exploited: (i) gene knockouts or transgenes in mice that result in specific phenotypes associated with mammary gland (143 loci); (ii) cattle QTL for milk production (344) and mastitis related traits (71); (iii) loci with sequence variations that show specific allele-phenotype interactions associated with milk production (24) or mastitis (10) in cattle; (iv) genes with expression profiles associated with milk production (207) or mastitis (107) in cattle or mouse; (v) cattle milk protein genes that exist in different genetic variants (9); (vi) miRNAs expressed in bovine mammary gland (32) and (vii) epigenetically regulated cattle genes associated with mammary gland function (1). Fourty-four genes found by multiple independent analyses were suggested as the most promising candidates and were further in silico analysed for expression levels in lactating mammary gland, genetic variability and top biological functions in functional networks. A miRNA target search for mammary gland expressed miRNAs identified 359 putative binding sites in 3'UTRs of candidate genes.

Detection of QTL for milk protein percentage in Italian Friesian cattle by AFLP markers and selective genotyping

We targeted quantitative trait loci (QTL) for milk protein percentage (P%) in two Italian Holstein granddaughter design families using selective genotyping in combination with high throughput amplified fragment length polymorphism (AFLP) markers. A total of 64 extreme high and low sires in respect to estimated breeding value (EBV) for P% (EBVP%) were genotyped with 25 AFLP primer combinations that revealed 305 and 291 polymorphisms in the two families. Association between markers and EBVP% was investigated by a linear model only on bands having paternal origin (105 and 96 AFLP bands in family D and S, respectively). Although no marker was significantly associated with the target trait after correction for multiple comparisons, 17 AFLP markers, significant without correction for multiple tests, were considered suggestive of the presence of a QTL. Eleven of these were successfully located on six Bos taurus (BTA) chromosomes by radiation hybrid or in-silico mapping. Ten of these mapped in the immediate neighbourhood (less than 10 cM) of already described QTL for P%. Suggestive association was verified in four regions by microsatellites analysis: one on BTA 10; one on BTA 28; and two on BTA 18. Microsatellites identified significant effects by single marker and interval mapping analyses on BTA 10 and BTA 28, while they were only suggestive of the presence of QTL on BTA 18. In summary, our results firstly indicate that AFLP markers may be used to seek QTL exploiting a selective genotyping approach in GDD, a wide used experimental design in cattle; secondly, propose two approaches for AFLP mapping, namely in-silico mapping exploiting most updated release from the bovine whole genome sequencing project, and physical mapping exploiting a panel of Bovine/Hamster Radiation Hybrids; and thirdly, provide new information on QTLs for an economic important trait in a never investigated Holstein cattle population. AFLP in combination with selective genotyping can be a useful strategy for QTL searching in minor livestock species, sometimes having large economic impact in marginal areas, where more informative markers are still poorly developed.