Pre-selection against a lethal recessive allele in breeding schemes with optimum-contribution selection or truncation selection

Background We tested the hypothesis that breeding schemes with a pre-selection step, in which carriers of a lethal recessive allele (LRA) were culled, and with optimum-contribution selection (OCS) reduce the frequency of a LRA, control rate of inbreeding, and realise as much genetic gain as breeding schemes without a pre-selection step. Methods We used stochastic simulation to estimate true genetic gain realised at a 0.01 rate of true inbreeding (ΔFtrue) by breeding schemes that combined one of four pre-selection strategies with one of three selection strategies. The four pre-selection strategies were: (1) no carriers culled, (2) male carriers culled, (3) female carriers culled, and (4) all carriers culled. Carrier-status was known prior to selection. The three selection strategies were: (1) OCS in which $$\Delta {\text{F}}_{{{\text{true}}}}$$ Δ F true was predicted and controlled using pedigree relationships (POCS), (2) OCS in which $$\Delta {\text{F}}_{{{\text{true}}}}$$ Δ F true was predicted and controlled using genomic relationships (GOCS), and (3) truncation selection of parents. All combinations of pre-selection strategies and selection strategies were tested for three starting frequencies of the LRA (0.05, 0.10, and 0.15) and two linkage statuses with the locus that has the LRA being on a chromosome with or without loci affecting the breeding goal trait. The breeding schemes were simulated for 10 discrete generations (t = 1, …, 10). In all breeding schemes, ΔFtrue was calibrated to be 0.01 per generation in generations t = 4, …, 10. Each breeding scheme was replicated 100 times. Results We found no significant difference in true genetic gain from generations t = 4, …, 10 between breeding schemes with or without pre-selection within selection strategy. POCS and GOCS schemes realised similar true genetic gains from generations t = 4, …, 10. POCS and GOCS schemes realised 12% more true genetic gain from generations t = 4, …, 10 than truncation selection schemes. Conclusions We advocate for OCS schemes with pre-selection against the LRA that cause animal suffering and high costs. At LRA frequencies of 0.10 or lower, OCS schemes in which male carriers are culled reduce the frequency of LRA, control rate of inbreeding, and realise no significant reduction in true genetic gain compared to OCS schemes without pre-selection against LRA.

Inheritance of evolved thiocarbamate resistance in Rigid Ryegrass (Lolium rigidum) populations from Australia

Populations of rigid ryegrass (Lolium rigidum Gaudin) from southern Australia have evolved resistance to the thiocarbamate herbicide prosulfocarb. The inheritance of prosulfocarb resistance was explored by crossing R and S individuals. In all families within each cross, except 16.2, the response of the F1 were intermediate between the parents, suggesting that resistance is inherited as a single, partially dominant trait. For 16.2, the response of the F1 was more similar to the susceptible parent, suggesting resistance may be a recessive trait in this population. Segregation at the discriminating dose of 1200 g a.i. ha−1 prosulfocarb in populations 375-14 fitted the ratio (15:1) consistent with two independent dominant alleles; 198-15 fitted a ratio (13:3) for two independent alleles, one dominant and one recessive; and EP162 fitted a ratio (9:7) for two additive dominant alleles. In contrast segregation of population 16.2 fitted a (7:9) ratio consistent with two independent recessive alleles contributing to prosulfocarb resistance. Four different patterns of resistance to prosulfocarb were identified in different resistant populations, with inheritance as a dominant allele, dominant and recessive, additive dominant and as an independent recessive allele. This suggests there are several different mechanisms of prosulfocarb resistance present in L. rigidum.

Simple inheritance of color and pattern polymorphism in the steppe grasshopper Chorthippus dorsatus

The green–brown polymorphism of grasshoppers and bush-crickets represents one of the most penetrant polymorphisms in any group of organisms. This poses the question of why the polymorphism is shared across species and how it is maintained. There is mixed evidence for whether and in which species it is environmentally or genetically determined in Orthoptera. We report breeding experiments with the steppe grasshopper Chorthippus dorsatus, a polymorphic species for the presence and distribution of green body parts. Morph ratios did not differ between sexes, and we find no evidence that the rearing environment (crowding and habitat complexity) affected the polymorphism. However, we find strong evidence for genetic determination for the presence/absence of green and its distribution. Results are most parsimoniously explained by three autosomal loci with two alleles each and simple dominance effects: one locus influencing the ability to show green color, with a dominant allele for green; a locus with a recessive allele suppressing green on the dorsal side; and a locus with a recessive allele suppressing green on the lateral side. Our results contribute to the emerging contrast between the simple genetic inheritance of green–brown polymorphisms in the subfamily Gomphocerinae and environmental determination in other subfamilies of grasshoppers. In three out of four species of Gomphocerinae studied so far, the results suggest one or a few loci with a dominance of alleles allowing the occurrence of green. This supports the idea that brown individuals differ from green individuals by homozygosity for loss-of-function alleles preventing green pigment production or deposition.

Segregation of Flower Color and Eyespot in Althea

Althea (Hibiscus syriacus) is an ornamental shrub prized for its winterhardiness, flower colors, and unique flower forms, including single-flowered and double-flowered types. Although floral traits are most important for breeders of althea, little is known about their segregation patterns. The objective of this study was to determine segregation patterns in flower color, including eyespot, among hybrid seedlings of elite taxa. Over 4 years, more than 3100 flowering seedlings were produced for observation of F1, F2, and backcross families. For each plant, data were collected including presence of eyespot and petal body color (CIEL*a*b*) using a colorimeter. Recessive testcrosses and χ2 analyses were performed among three taxa (‘Buddha Belly’, ‘Diana’, and White Chiffon®), and between this recessive group and a suite of colorful taxa. Self-pollination and intercrosses within homozygous dominant and homozygous recessive groups further confirmed their genotypes. Based on these results, we propose that eyespot is controlled by a single gene called spotless, named for the recessive allele that results in a complete elimination of color in flowers. Crosses that resulted in seedlings that all produced eyespots were observed to segregate for color in the petal body. Of these, one group produced white to blush pink petals, which was recessive to full color. Recessive testcrosses and χ2 analyses were performed among nine taxa exhibiting eyespots with white to blush petal bodies, and between taxa with full-color petal bodies. These testcrosses resulted in a putative homozygous dominant group composed mostly of blue and dark pink taxa, whereas the heterozygous group was composed mostly of pink taxa. Spotless taxa were also added to these two groups, suggesting an epistatic interaction with the spotless allele. Based on these results, we propose that petal body color is controlled by a single gene called geisha, named for the recessive allele that produces white to blush-pink petal bodies and dark red eyespot. This trait exhibits incomplete dominance and is under epistatic control by spotless. Geisha-type flowers lack pigment in the petal body, or exhibit a blush pink, likely produced by low levels of cyanidin, peonidin, and pelargonidin. The interaction and segregation of these two genes was confirmed in F1, F2, and backcross families from two crosses: Lil’ Kim™ × Blue Chiffon™ and Fiji™ × White Chiffon®. This study on segregation of flower color in H. syriacus contributes substantial and useful information on inheritance of color and will facilitate targeted breeding to improve this vibrant ornamental shrub.

Inbreeding in a Family Tree and in a Population

On the basis of Hardy – Weinberg’s law the problem of inbreeding in a family tree and a population was investigated. With use of an inbreeding factor are received the discrete equation for a family tree and differential equation for a population. The numerical solution of the differential equation for a population was found and analyzed at various values of the inbreeding factor. Migration of inbred population is investigated in view of natural selection. It was shown that velocity of migration falls with increase of the inbreeding factor. Interrelation of the recessive allele frequency at woman for a migrating population with inbreeding factor and standard parameter of selection was found.

Identification of allelic combinations of the Ppd-D1, Vrn-A1, Vrn-B1 and Vrn-D1 genes in common wheat lines obtained in the National Center of Grain named after P. P. Lukyanenko

An analysis of the allelic composition of the genes determining photoperiodic sensitivity (Ppd-D1) and the need for vernalization (Vrn-A1, Vrn-B1, Vrn-D1) was carried out in 286 common wheat lines obtained in the National Center of Grain named after P. P. Lukyanenko with the use of allele-specific primers. The analyzed samples were distributed over 21 haplotypes; the dominant allele of the Ppd-D1a gene prevailed in the studied material. 123 lines of common wheat carry a combination of D-RRD alleles. The lines that can be attributed to the group of alternate wheat (R-RDR, R-RRD) were identified. All studied samples carry the recessive allele of at least one VRN1 gene.

Association between coat colour and the behaviour of Australian Labrador retrievers

Background Making assumptions regarding temperament and intelligence based on the physical appearance of dogs can be a conscious or unconscious human act. Labrador retrievers with chocolate-coloured coats are anecdotally considered to be less trainable and more hyperactive and aggressive than their black or yellow peers. To test these assertions, we analysed the owner-reported behavioural traits of Labradors in relation to both their observable coat colour, and their TYRP1 and MC1R genotypes. Results We used the results of an owner-based questionnaire to determine scores for 21 behavioural traits and test whether these scores varied with coat colour (n = 225). Familiar dog aggression was the only trait that was found to vary significantly with coat colour (P = 0.013). Yellow Labradors had a higher score than chocolate Labradors, even when corrected for multiple testing (P = 0.021). We repeated the analyses for a subset of 63 Labradors with available genotyping data for the genes (MC1R and TYRP1) that are known to determine the primary coat colours in Labradors. Familiar dog aggression scores varied with both the observed coat colour and MC1R genotype. Dogs homozygous for MC1R recessive allele (with yellow coat colour) scored higher for familiar dog aggression than either black or chocolate Labradors. However, no association maintained significance when incorporating Bonferroni correction. Dog trainability scores decreased additively as the number of recessive brown alleles for TYRP1 increased. This allelic association was independent of the observable coat colour. Dogs homozygous for the brown allele were considered less trainable than dogs with no brown alleles (P = 0.030). Conclusions Our results do not support that chocolate-coloured Labradors are more hyperactive or aggressive than either black or yellow Labradors. Trainability scores varied with TYRP1 genotype but not the observable coat colour. Further validation is required.

Development and validation of breeder-friendly functional markers of sugary1 gene encoding starch-debranching enzyme affecting kernel sweetness in maize (Zea mays)

The sweet corn variety of maize (Zea mays L.) has become popular worldwide. The recessive allele of sugary1 (su1) encoding starch de-branching enzyme has been much used for sweet corn cultivar development. Here, we aimed to develop su1-based functional marker(s) by using six diverse inbred lines of sugary type and five inbred lines of wild type, and using 27 overlapping primers. In total, 12 indels (insertion and deletion) and 96 SNPs (single nucleotide polymorphisms) were identified that clearly differentiated the dominant and recessive allele of su1. Among these, a 36-bp indel (at position 1247) in the promoter region included a TATA-box, and a 6-bp indel (at position 6456) in intron-10 was predicted to have SRp40 exon-splicing enhancer. Nucleotide substitution in exon-2 at position 2703 (SNP-2703) was involved in C to G mutation leading to conversion of phenylalanine to leucine. The 6-bp and 36-bp indels and SNP-2703 were used to develop breeder-friendly codominant markers: SuDel6-FR, SuDel36-FR and SNP2703-CG-85/89. All three markers were validated in five F2 populations, and SuDel36-FR and SNP2703-CG-85/89 were validated in a set of 230 diverse inbreds having both mutant and wild-type alleles of Su1. This is the first report of development and validation of universal functional markers for su1. These markers (SuDel36-FR and SNP2703-CG-85/89) assume great significance in marker-assisted breeding program.