Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm.

Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs.The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species.

Cloning of the papaya chromoplast-specific lycopene beta-cyclase, CpCYC-b, controlling fruit flesh color reveals conserved microsynteny and a recombination hot spot.

Carotenoid pigments in fruits are indicative of the ripening process and potential nutritional value. Papaya (Carica papaya) fruit flesh color is caused by the accumulation of lycopene or beta-carotenoids in chromoplasts. It is a distinct feature affecting nutritional composition, fruit quality, shelf life, and consumer preference. To uncover the molecular basis of papaya flesh color, we took map-based cloning and candidate gene approaches using integrated genetic and physical maps. A DNA marker tightly linked to flesh color colocalized on a contig of the physical map with a cDNA probe of the tomato (Solanum lycopersicum) chromoplast-specific lycopene beta-cyclase, CYC-b. Candidate gene sequences were obtained from amplified fragments and verified by sequencing two bacterial artificial chromosomes containing the two alleles. Sequence comparison revealed a 2-bp insertion in the coding region of the recessive red flesh allele resulting in a frame-shift mutation and a premature stop codon. A color complementation test in bacteria confirmed that the papaya CpCYC-b is the gene controlling fruit flesh color. Sequence analysis of wild and cultivated papaya accessions showed the presence of this frame-shift mutation in all red flesh accessions examined. Evaluation of DNA markers near CpCYC-b revealed a recombination hot spot, showing that CpCYC-b is located in a gene-rich region with a recombination rate at 3.7 kb per centimorgan, more than 100-fold higher than the genome average at 400 kb per centimorgan. Conserved microsynteny of the CpCYC-b region is indicated by colinearity of two to four genes between papaya, Arabidopsis (Arabidopsis thaliana), grape (Vitis vinifera), and tomato. Our results enhanced our understanding of papaya flesh color inheritance and generated new tools for papaya improvement.

Enrichment of a papaya high-density genetic map with AFLP markers.

A high-density genetic linkage map of papaya, previously developed using an F2 mapping population derived from the intraspecific cross AU9 x SunUp, was enriched with AFLP markers. The comprehensive genetic map presented here spans 945.2 cM and covers 9 major and 5 minor linkage groups containing 712 SSR, 277 AFLP, and 1 morphological markers. The average marker density for the 9 major linkage groups is 0.9 cM between adjacent markers, and the total number of gaps >5 cM was reduced from 48 to 27 in the current map. AFLPs generated by EcoRI/MseI primer combinations were distributed throughout the 14 linkage groups and resulted in several large locus order rearrangements within the 9 major linkage groups. Integration of AFLP markers provided tighter linkage association between loci, leading to a reduction in map distance on LGs 1, 2, and 4, which were inflated in the previous map, and correction of the marker order on LG8. Suppression of recombination in the male-specific Y region (MSY) of LG1 is further validated by the addition of 27 sex co-segregating AFLP markers. A large region of distorted segregation surrounding the MSY spans 54.4 cM and represents approximately 71% of the linkage group. This comprehensive high-density genetic map provides a framework for mapping quantitative trait loci and for fine mapping as well as for comparative genomic studies of crop plant development and evolution.