Quantitative trait loci and transcriptome signatures associated with avian heritable resistance to Campylobacter

Campylobacter is the leading cause of bacterial foodborne gastroenteritis worldwide. Handling or consumption of contaminated poultry meat is a key risk factor for human campylobacteriosis. One potential control strategy is to select poultry with increased resistance to Campylobacter. We associated high-density genome-wide genotypes (600K single nucleotide polymorphisms) of 3000 commercial broilers with Campylobacter load in their caeca. Trait heritability was modest but significant (h2 = 0.11 ± 0.03). Results confirmed quantitative trait loci (QTL) on chromosomes 14 and 16 previously identified in inbred chicken lines, and detected two additional QTLs on chromosomes 19 and 26. RNA-Seq analysis of broilers at the extremes of colonisation phenotype identified differentially transcribed genes within the QTL on chromosome 16 and proximal to the major histocompatibility complex (MHC) locus. We identified strong cis-QTLs located within MHC suggesting the presence of cis-acting variation in MHC class I and II and BG genes. Pathway and network analyses implicated cooperative functional pathways and networks in colonisation, including those related to antigen presentation, innate and adaptive immune responses, calcium, and renin–angiotensin signalling. While co-selection for enhanced resistance and other breeding goals is feasible, the frequency of resistance-associated alleles was high in the population studied and non-genetic factors significantly influenced Campylobacter colonisation.

The genetic relationship among plant-height traits found using multiple-trait QTL mapping of a dent corn and popcorn cross

Plant height (PH) is one of the most important traits in maize breeding programs. In popcorn, inferior plant traits can be improved with the dent/flint corn germplasm. In the current study, a total of 259 F2:3 families, developed from a cross between a dent corn inbred and a popcorn inbred, were evaluated for 4 PH traits. Quantitative trait loci (QTLs) for each trait were detected using composite interval mapping methods. In addition, genetic interrelationships were investigated using multiple-trait joint analysis for PH with ear height (EH), and for PH with top height (TH). In total, 6, 5, 2, and 6 QTLs were identified for PH, EH, TH, and TH/PH in single-trait analysis, respectively. Joint-analysis data suggest a strong and complex genetic relationship between PH and EH, and between PH and EH, with no QTLs controlling any single trait independently. In addition, 4 kinds of QTLs detected were classified as closely linked QTLs, pleiotropic QTLs, QTLs with opposite effects, and additional QTLs. It was, consequently, difficult to improve lodge resistance through selection on any individual PH trait. The current study demonstrates that multiple-trait joint analysis not only identified additional QTLs, but also revealed the genetic relationship among different highly correlated traits at the molecular level.

Chromosome 2 Reciprocal Congenics to Evaluate the Effect of the Genetic Background on Blood Pressure

54 Background Localisation of QTL using a genome wide scan strategy is the first step towards gene identification. This is followed by the construction of congenics by which the existence of the QTL can be verified. Congenic strains for chromosome 2 using the Dahl S as the recipient and WKY and MNS as donors, showed variable blood pressure (BP) depending on the donor alleles 1 . Methods We used a speed congenic approach to produce several congenic strains of chromosome 2 using the SHRSP Gla and the WKY Gla as recipients to test the effect of the genetic background of a given congenic on BP. In some strains, the region introgressed was identical to avoid confounding effects of additional QTLs. Two reciprocal control congenic strains were also produced to determine the presence of any passenger loci. Baseline systolic BP was measured by radiotelemetry. Results Four congenic and 2 parental strains were phenotyped (n=3-6). Transfer of the region of rat chromosome 2 from the WKY into a SHRSP background significantly lowered both day and night-time systolic BP by approximately 16 and 20 mm Hg respectively in male congenic rats compared to the SHRSP parental strains (p<0.005, 95%CI: 8.6-21.0 mm Hg; and p<0.005, 95%CI: 16.7-24.7 mm Hg). In contrast, transfer of the same region from the SHRSP into a WKY background significantly increased both day and night-time systolic BP by approximately 25 and 28 mm Hg, respectively in male congenic rats compared to the WKY parental strains (p<0.05, 95%CI: -49.2-2.0 mmHg; and p<0.05%, 95%CI: -61.2-6.1 mm Hg, respectively). Reciprocal control congenic strain showed no deviation from the BP recorded in the parental strain (Strain WKY.SPGla2b vs. WKY parental strain, 128.8±5.2 mm Hg vs. 139.7±5.7 mm Hg, p= ns; and strain SP.WKYGla2b vs. SHRSP parental strain, 178.0±5.0 mm Hg vs. 179.9±2.1 mm Hg, p= ns). Conclusions The results show the effect of a permissive background on BP and confirm that the genetic background chosen for a congenic strain has a significant effect on the BP phenotype. Moreover, this work sheds new light on the different epistatic or pleiotropic effects according to the genetic background chosen. 1. Deng AY et al . Hypertension 1997;30:199-202

D-Subgenome Bias of Xcm Resistance Genes in Tetraploid Gossypium (Cotton) Suggests That Polyploid Formation Has Created Novel Avenues for Evolution

A detailed RFLP map was used to determine the chromosomal locations and subgenomic distributions of cotton (Gossypium) genes/QTLs that confer resistance to the bacterial blight pathogen, Xanthomonas campestris pv. malvacearum (Xcm). Genetic mapping generally corroborated classic predictions regarding the number and dosage effects of genes conferring Xcm resistance. One recessive allele (b6) was a noteworthy exception to the genetic dominance of most plant resistance alleles. This recessive allele appeared to uncover additional QTLs from both resistant and ostensibly susceptible genotypes, some of which corresponded in location to resistance (R)-genes effective against other Xcm races. One putatively “defeated” resistance allele (B3) reduced severity of Xcm damage by “virulent” races. Among the six resistance genes derived from tetraploid cottons, five (83%) mapped to D-subgenome chromosomes—if each subgenome were equally likely to evolve new R-gene alleles, this level of bias would occur in only about 1.6% of cases. Possible explanations of this bias include biogeographic factors, differences in evolutionary rates between subgenomes, gene conversion or other intergenomic exchanges that escaped detection by genetic mapping, or other factors. A significant D-subgenome bias of Xcm resistance genes may suggest that polyploid formation has offered novel avenues for phenotypic response to selection.

Interval mapping of multiple quantitative trait loci.

The interval mapping method is widely used for the mapping of quantitative trait loci (QTLs) in segregating generations derived from crosses between inbred lines. The efficiency of detecting and the accuracy of mapping multiple QTLs by using genetic markers are much increased by employing multiple QTL models instead of the single QTL models (and no QTL models) used in interval mapping. However, the computational work involved with multiple QTL models is considerable when the number of QTLs is large. In this paper it is proposed to combine multiple linear regression methods with conventional interval mapping. This is achieved by fitting one QTL at a time in a given interval and simultaneously using (part of) the markers as cofactors to eliminate the effects of additional QTLs. It is shown that the proposed method combines the easy computation of the single QTL interval mapping method with much of the efficiency and accuracy of multiple QTL models.