An updated Axiom buffalo genotyping array map and mapping of cattle quantitative trait loci to the new water buffalo reference genome assembly.

The objectives of this study were to provide the buffalo research community with an updated SNP map for the Axiom Buffalo Genotyping (ABG) array with genomic positions for SNP currently unmapped and to map all cattle QTL from the CattleQTLdb onto the buffalo reference assembly. To update the ABG array map, all SNP probe sequences from the ABG array were re-aligned against the UOA_WB_1 assembly. With the new map, the number of mapped markers increased by approximately 10% and went from 106 778 to 116 708, which reduced the average marker spacing by approximately 2 kb. A comparison of results between signatures of autozygosity study using the ABG and the new map showed that, when the additional markers were used there was an increase in the autozygosity peaks and additional peaks in BBU5 and BBU11 could be identified. After sequence alignment and quality control, 64 650 (UMD3.1) and 76 530 (ARS_UCD1.2) cattle QTL were mapped onto the buffalo genome. The mapping of the bovine QTL database onto the buffalo genome should be useful for genome-wide association studies in buffalo and, given the high homology between the two species, the positions of cattle QTL on the buffalo genome can serve as a stepping stone towards a water buffalo QTL database.

Identification of QTLs Linked to Phenological and Morphological Traits in RILs Population of Horsegram (Macrotyloma uniflorum).

Horsegram [Macrotyloma uniflorum (Lam.) Verdc.] is an important legume but understudied in terms of its genetic improvement. Genetic information on various phenological and morphological traits may help in the utilization of new genes for breeding in horsegram and thus affect agronomic practices and crop yield. A total of 162 recombinant inbred lines derived from intraspecific crosses between HPKM249 × HPK4 was used to construct a genetic linkage map and to identify quantitative trait loci (QTLs) associated with phenological and morphological traits. Of the total 2011 molecular markers, which were screened on parental lines for polymorphism survey, 493 markers were found to be polymorphic and used for genotyping of recombinant inbred line population. Out of 493 polymorphic markers, 295 were mapped on ten linkage groups at LOD 3.5 spanning a total distance of 1,541.7 cM with an average distance between markers of 5.20 cM. Phenotypic data of two years at two different locations were used to identify QTLs by composite interval mapping A total of four QTLs (LOD ≥2.5) for phenological traits (days to 50% flowering, reproductive period and days to maturity) and seven QTLs (LOD ≥2.5) for morphological traits (plant height, primary branches and secondary branches) were detected across different environments. The phenotypic variation explained by QTLs ranged from 6.36 to 47.53%. The present study will help to augment scanty genomic information in this orphan crop that would provide genomics tools to breeders for its genetic enhancement through molecular-assisted selection.