Genotyping by target sequencing (GBTS) integrates the advantages of silicon-based technology (high stability and reliability) and genotyping by sequencing (high flexibility and cost-effectiveness).  However, GBTS panels are not currently available in pigs.  In this study, based on GBTS technology, we first developed a 50K panel, including 52,000 single-nucleotide polymorphisms (SNPs), in pigs, designated GBTS50K.  A total of 6,032 individuals of Large White, Landrace, and Duroc pigs from 10 breeding farms were used to assess the newly developed GBTS50K.  Our results showed that GBTS50K obtained a high genotyping ability, the SNP and individual call rates of GBTS50K were 0.997–0.998, and the average consistency rate and genotyping correlation coefficient were 0.997 and 0.993, respectively, in replicate samples.  We also evaluated the efficiencies of GBTS50K in the application of population genetic structure analysis, selection signature detection, genome-wide association studies (GWAS), genotyped imputation, genetic selection (GS), etc.  The results indicate that GBTS50K is plausible and powerful in genetic analysis and molecular breeding.  For example, GBTS50K could gain higher accuracies than the current popular GGP-Porcine bead chip in genomic selection on 2 important traits of backfat thickness at 100 kg and days to 100 kg in pigs.  Particularly, due to the multiple SNPs (mSNPs), GBTS50K generated 100K qualified SNPs without increasing genotyping cost, and our results showed that the haplotype-based method can further improve the accuracies of genomic selection on growth and reproduction traits by 2 to 6%.  Our study showed that GBTS50K could be a powerful tool for underlying genetic architecture and molecular breeding in pigs, and it is also helpful for developing SNP panels for other farm animals.

Introducing the inherent genetic diversity of wild species into cultivars has become one of the hot topics in crop genetic breeding and genetic resource research.  Fiber- and seed-related traits, which are critical to the global economy and people’s livelihoods, are the principal focus of cotton breeding.  Here, the wild cotton species Gossypium tomentosum was used to broaden the genetic basis of G. hirsutum and identify QTLs for fiber- and seed-related traits.  A population of 559 chromosome segment substitution lines (CSSLs) was established with various chromosome segments from G. tomentosum in a G. hirsutum cultivar background.  Totals of 72, 89, and 76 QTLs were identified for three yield traits, five fiber quality traits, and six cottonseed nutrient quality traits, respectively.  Favorable alleles of 104 QTLs were contributed by G. tomentosum.  Sixty-four QTLs were identified in two or more environments, and candidate genes for three of them were further identified.  The results of this study contribute to further studies on the genetic basis of the morphogenesis of these economic traits, and indicate the great breeding potential of G. tomentosum for improving the fiber- and seed-related traits in G. hirsutum.

Cotton is an important natural fiber crop worldwide which plays a vital role in our daily life.  High yield is a constant goal of cotton breeding, and lint percentage (LP) is one of the important components of cotton fiber yield.  A stable QTL controlling LP, qLP_A01.1, was identified on chromosome A01 from Gossypium hirsutum introgressed lines with G. tomentosum chromosome segments in a previous study.  To fine-map qLP_A01.1, an F₂ population with 986 individuals was established by crossing G. hirsutum cultivar CCRI35 with the chromosome segment substitution line HT_390.  A high-resolution genetic map including 47 loci and spanning 56.98 cM was constructed in the QTL region, and qLP_A01.1 was ultimately mapped into an interval corresponding to an ~80 kb genome region of chromosome A01 in the reference genome, which contained six annotated genes.  Transcriptome data and sequence analysis revealed that S-acyltransferase protein 24 (GoPAT24) might be the target gene of qLP_A01.1.  This result provides the basis for cotton fiber yield improvement via marker-assisted selection (MAS) and further studies on the mechanism of cotton fiber development.