CASE1—— Prunus persica Genome and Resequencing The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Genetics. Published online: 24 March 2013 | doi:10.1038/ng.2586 Results The high-quality genome sequence of peach obtained from a completely homozygous genotype through complete chromosome-scale assembly using Sanger whole-genome shotgun methods. Investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions, which suggesting major genetic bottlenecks that have substantially shaped peach genome diversity Comparative analyses showed that peach has not undergone recent whole-genome duplication Material and methods double haploid genotype of the peach cv. Lovell (PLov2-2N; 2n = 2x = 16) 11 P. persica accessions (including the dihaploid Lovell PLov2-2N) and Prunus ferganensis, Prunus kansuensis, Prunus davidiana and Prunus mira Research Objective Obtain the reference assembly Examine the genomic path of peach domestication by genome re-sequencing

Peach chromosome-scale final summary statistics Peach v1.0 chromosome-scale final summary statistics Final summary assembly statistics for the upcoming refined chromosome-scale release. Peach chromosome-scale final summary statistics

Figure 2 Nucleotide diversity distribution in peach. Fivefold higher density of genes encoding the NB-LRR proteins compared to the rest of the genome. The outer track represents nucleotide diversity (π) in 50-kb nonoverlapping sliding windows estimated from a sample of 23 haploid genotypes (11 diploid accessions and the reference dihaploid Lovell). The 14 inner tracks depict the SNP frequency distributions for 50-kb nonoverlapping sliding windows in the ten peach accessions and four Prunus wild species compared to the reference individual (dihaploid Lovell). Fruit maturity time Figure 2 Nucleotide diversity distribution in peach.

Peach has not undergone recent whole-genome duplication Figure 4 Distribution of 4DTv distance between syntenic gene pairs among peach, apple and grapevine. Figure 3 Duplicated and triplicated regions in the peach genome. Each line links duplicated regions in peach. The seven different colors represent each linkage group of the eudicot ancestor that existed before hexaploidization. Peach genomic regions are colored by their orthology to the grape genome. The lines are colored by the paralogous regions, and the order of precedence when paralogous regions have different ancestral origins is indicated by the colors of TR1, TR2, TR3, TR4, TR5, TR6, TR7 and gray. Seven major triplicated regions (TR1–TR7) are shown.PC, Prunus chromosome. Figure 4 Distribution of 4DTv distance between syntenic gene pairs among peach, apple and grapevine. Segments of homologous genes were found by locating blocks of BLASTP hits with an E value of 1 × 10−10 or better with less than five intervening genes between such hits. The 4DTv distance between orthologous genes on these segments is shown. Figure 3 Duplicated and triplicated regions in the peach genome. Peach has not undergone recent whole-genome duplication

Polyol biosynthesis and phenylpropanoid metabolism A6PR (aldose 6-P reductase, which is rate limiting for sorbitol biosynthesis) SDH (sorbitol dehydrogenase, which converts the alcohol into sugars in fruits) SOT (sorbitol transporters ) p-coumarate 3-hydroxylase (the rate-limiting enzyme in monolignol biosynthesis, encoded by C3H) hydroxycinnamyl transferases (encoded by HCT and HQT) In contrast to other species, apple and peach SDH and SOT are large gene families; Peach with no recent whole-genome duplication; C3H: 5 members (4 arranged in small tandem duplications on PC 1 HCT and HQT: also expanded (11 members in total) due to tandem duplication events in PC 3 (10) This specific gene family expansions probably occurred before the evolutionary split of the genera Malus and Prunus. the tandem gene duplication events in these two important gene families in phenylpropanoid metabolism are probably associated with specialization Polyol biosynthesis and phenylpropanoid metabolism

CASE2——Sorghum resequencing Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biology. 2011, 12:R114. Sorghum (Sorghum bicolor) is globally produced as a source of food, feed, fibre and fuel. Grain and sweet sorghums differ in a number of important traits including stem sugar and juice accumulation, plant height as well as grain and biomass production. The first whole genome sequence of a grain sorghum is available, but additional genome sequences are required to study genome-wide and intraspecific variation for dissecting the genetic basis of these important traits and for tailor-designed breeding of this important C4 crop. We resequenced two sweet and one grain sorghum inbred lines, and identified a set of nearly 1,500 genes differentiating sweet and grain sorghum. These genes fall into 10 major metabolic pathways involved in sugar and starch metabolisms, lignin and coumarin biosynthesis, nucleic acid metabolism, stress responses and DNA damage repair. In addition, we uncovered 1,057,018 SNPs, 99,948 indels of 1-10bp in length and 16,487 presence/absence variations as well as 17,111 CNVs. The majority of the large-effect SNPs, indels and presence/absence variations resided in the genes containing leucine rich repeats, PPR repeats and disease resistance R genes possessing diverse biological functions or under diversifying selection, but were absent in genes which are essential for life. This is a first report of the identification of genome-wide patterns of genetic variation in sorghum. High-density SNP and indel markers reported here will be a valuable resource for future gene - phenotype studies and the molecular breeding of this important crop and related species. Results average of approximately 12 depth for each sample identified ~1,500 genes differentiating sweet and grain sorghum. uncovered 1,057,018 SNPs, 99,948 indels of 1-10bp in length and 16,487 presence/absence variations as well as 17,111 CNVs Material and methods two sweet and one grain sorghum inbred lines Research Objective Detection of genetic variation in sweet and grain sorghum

Table 1. Agronomic and biofuel-associated traits of the sorghum lines used for resequencing

CASE3——Development and mapping of SNP assays in allotetraploid cotton Development and mapping of SNP assays in allotetraploid cotton. Theor Appl Genet (2012) 124:1201–1214. Results 1. 2.04 million reads were assembled into contigs with an N50 of 508 bp and analyzed for SNPs. 2.11,834 and 1,679 non-genic SNPs were identified between accessions of G. hirsutum and G. barbadense, respectively. 3. 4,327 genic SNPs were also identified between accessions of G. hirsutum in the EST assembly. 4. 367 markers mapped in a segregating F2 population (Acala Maxxa 9 TX2094) using the Fluidigm EP1 system. Brigham Young University Material and methods Two G. hirsutum and two G. barbadense. RAD (EcoRI, BafI double digest) 454 sequencing De novo Assembly and SNP calling Research Objective For SNP Discovery in a complex allotetraploid genome of cotton.

Fig. 1 SNP discovery flowchart for GR-RSC in allotetraploid cotton.

Fig. 2 Allotetraploid SNP identification.

Fig. 3 Distribution of contigs in the GR-RSC assemblies.

Fig. 4 F2 genotyping plots from the Fluidigm SNP Genotyping Analysis software.