Genome-wide association studies (GWAS) were undertaken to identify SNP markers associated with yield and yield-related traits in 123 Pakistani historical wheat cultivars evaluated during 2011–2014 seasons under rainfed field conditions. The population was genotyped by using high-density Illumina iSelect 90K single nucleotide polymorphism (SNP) assay, and finally 14,960 high quality SNPs were used in GWAS. Population structure examined using 1000 unlinked markers identified seven subpopulations (K = 7) that were representative of different breeding programs in Pakistan, in addition to local landraces. Forty four stable marker-trait associations (MTAs) with -log p > 4 were identified for nine yield-related traits. Nine multi-trait MTAs were found on chromosomes 1AL, 1BS, 2AL, 2BS, 2BL, 4BL, 5BL, 6AL, and 6BL, and those on 5BL and 6AL were stable across two seasons. Gene annotation and syntey identified that 14 trait-associated SNPs were linked to genes having significant importance in plant development. Favorable alleles for days to heading (DH), plant height (PH), thousand grain weight (TGW), and grain yield (GY) showed minor additive effects and their frequencies were slightly higher in cultivars released after 2000. However, no selection pressure on any favorable allele was identified. These genomic regions identified have historically contributed to achieve yield gains from 2.63 million tons in 1947 to 25.7 million tons in 2015. Future breeding strategies can be devised to initiate marker assisted breeding to accumulate these favorable alleles of SNPs associated with yield-related traits to increase grain yield. Additionally, in silico identification of 454-contigs corresponding to MTAs will facilitate fine mapping and subsequent cloning of candidate genes and functional marker development.

The high resolution integration of bread wheat genetic and genomic resources accumulated during the last decades offers the opportunity to unveil candidate genes driving major agronomical traits to an unprecedented scale. We combined 27 public quantitative genetic studies and four genetic maps to deliver an exhaustive consensus map consisting of 140,315 molecular markers hosting 221, 73, and 82 Quantitative Trait Loci (QTL) for respectively yield, baking quality, and grain protein content (GPC) related traits. Projection of the consensus genetic map and associated QTLs onto the wheat syntenome made of 99,386 genes ordered on the 21 chromosomes delivered a complete and non-redundant repertoire of 18, 8, 6 metaQTLs for respectively yield, baking quality and GPC, altogether associated to 15,772 genes (delivering 28,630 SNP-based makers) including 37 major candidates. Overall, this study illustrates a translational research approach in transferring information gained from grass relatives to dissect the genomic regions hosting major loci governing key agronomical traits in bread wheat, their flanking markers and associated candidate genes to be now considered as a key resource for breeding programs.

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Monogenic forms of obesity have been identified in ≤10% of severely obese European patients. However, the overall spectrum of deleterious variants (point mutations and structural variants) responsible for childhood severe obesity remains elusive. In this study, we genetically screened 225 severely obese children from consanguineous Pakistani families through a combination of techniques, including an in-house–developed augmented whole-exome sequencing method (CoDE-seq) that enables simultaneous detection of whole-exome copy number variations (CNVs) and point mutations in coding regions. We identified 110 (49%) probands carrying 55 different pathogenic point mutations and CNVs in 13 genes/loci responsible for nonsyndromic and syndromic monofactorial obesity. CoDE-seq also identified 28 rare or novel CNVs associated with intellectual disability in 22 additional obese subjects (10%). Additionally, we highlight variants in candidate genes for obesity warranting further investigation. Altogether, 59% of cases in the studied cohort are likely to have a discrete genetic cause, with 13% of these as a result of CNVs, demonstrating a remarkably higher prevalence of monofactorial obesity than hitherto reported and a plausible overlapping of obesity and intellectual disabilities in several cases. Finally, inbred populations with a high prevalence of obesity provide unique, genetically enriched material in the quest of new genes/variants influencing energy balance.

Canine monocytic ehrlichiosis is a tick-borne disease caused by an intracellular alpha-proteobacterium, Ehrlichia canis, which replicates within mononuclear cells in the host. This study was designed to use a polymerase chain reaction (PCR) protocol for the molecular detection of E. canis by the amplification of a portion of its 16S rRNA gene, as well as the effects of this alpha-proteobacterium on the haematological parameters of the sampled dogs and the risk factors associated with E. canis infection. A total of 151 blood samples were collected from dogs of various breeds at three sampling sites (Lahore, Rawalpindi/Islamabad and Multan) in Punjab, Pakistan. Data regarding the epidemiological factors (including age, gender, breed, body temperature, deworming, vaccination, mucous membrane status, hydration status, the presence of haematuria and tick infestation) were collected through a questionnaire at the time of sample collection. A 400 bp DNA fragment of the 16S rRNA gene of E. canis was amplified from 42 dog blood samples (28% of the total), [Lahore (N = 24), Rawalpindi/Islamabad (N = 13) and Multan (N = 05)] through PCR. Data analysis revealed that the character of the animals (age, sex and breed) had no significant association (P > 0.05) with the presence of E. canis. Various haematological parameters were also compared, and the results revealed that all of the parameters remained unaffected, except significantly lower white blood cell counts (P = 0.004) in E. canis-positive blood samples, as compared with the control group. We concluded that this is the first molecular confirmation of canine infection by E. canis using PCR. Moreover, no specific epidemiological parameter was found associated with the prevalence of E. canis in dogs.