A Data-Driven Approach to Sugarcane Breeding Programs with Agronomic Characteristics and Amino Acid Constituent Profiling.

Sugarcane (Saccharum spp. hybrids) and its processed products have supported local industries such as those in the Nansei Islands, Japan. To improve the sugarcane quality and productivity, breeders select better clones by evaluating agronomic characteristics, such as commercially recoverable sugar and cane yield. However, other constituents in sugarcane remain largely unutilized in sugarcane breeding programs. This study aims to establish a data-driven approach to analyze agronomic characteristics from breeding programs. This approach also determines a correlation between agronomic characteristics and free amino acid composition to make breeding programs more efficient. Sugarcane was sampled in clones in the later stage of breeding selection and cultivars from experimental fields on Tanegashima Island. Principal component analysis and hierarchical cluster analysis using agronomic characteristics revealed the diversity and variability of each sample, and the data-driven approach classified cultivars and clones into three groups based on yield type. A comparison of free amino acid constituents between these groups revealed significant differences in amino acids such as asparagine and glutamine. This approach dealing with a large volume of data on agronomic characteristics will be useful for assessing the characteristics of potential clones under selection and accelerating breeding programs.

Gene prediction for leaf margin phenotype and fruit flesh color in pineapple (Ananas comosus) using haplotype-resolved genome sequencing.

Pineapple (Ananas comosus (L.) Merr.) is one of the most economically important tropical fruit species. The major aim of the breeding programs in several countries, including Japan, is quality improvement, mainly for the fresh market. 'Yugafu', a Japanese cultivar with distinctive pipe-type leaf margin phenotype and white flesh color, is popular for fresh consumption. Therefore, genome sequencing of 'Yugafu' is expected to assist pineapple breeding. Here, we developed a haplotype-resolved assembly for the heterozygous genome of 'Yugafu' using long-read sequencing technology and obtained a pair of 25 pseudomolecule sequences inherited from the parental accessions 'Cream pineapple' and 'HI101'. The causative genes for leaf margin and fruit flesh color were identified. Fine mapping revealed a 162-kb region on CLG23 for the leaf margin phenotype. In this region, 20 kb of inverted repeat was specifically observed in the 'Cream pineapple' derived allele, and the WUSCHEL-related homeobox 3 (AcWOX3) gene was predicted as the key gene for leaf margin morphogenesis. Dominantly repressed AcWOX3 via RNAi was suggested to be the cause of the pipe-type leaf margin phenotype. Quantitative trait locus (QTL) analysis revealed that the terminal region of CLG08 contributed to white flesh and low carotenoid content. Carotenoid cleaved dioxygenase 4 (AcCCD4), a key gene for carotenoid degradation underlying this QTL, was predicted as the key gene for white flesh color through expression analysis. These findings could assist in modern pineapple breeding and facilitate marker-assisted selection for important traits.

Buckwheat R2R3 MYB transcription factor FeMYBF1 regulates flavonol biosynthesis.

Buckwheat (Fagopyrum esculentum) contains high amounts of flavonoids, especially flavonols (e.g., rutin), which are thought to be highly beneficial for human health. Little is known, however, about the regulation of flavonol synthesis in buckwheat. We identified a buckwheat gene encoding an R2R3 MYB transcription factor, and named this gene FeMYBF1. Analysis of the deduced amino acid sequence and phylogenetic analysis suggested that FeMYBF1 encodes an ortholog of the Arabidopsis flavonol regulators AtMYB11, AtMYB12 and AtMYB111. Expression of FeMYBF1 in a flavonol-deficient Arabidopsis triple mutant (myb11 myb12 myb111) restored flavonol synthesis. Constitutive expression of FeMYBF1 driven by the CaMV 35S promoter in Arabidopsis resulted in over-accumulation of flavonol glycosides and upregulation of the expression of AtFLS1. Transient expression assays showed that FeMYBF1 activated the promoter of the Arabidopsis gene encoding AtFLS1, and the promoters of buckwheat genes related to anthocyanin and proanthocyanidin synthesis such as dihydroflavonol 4-reductase (DFR) and leucoanthocyanidin dioxygenase (LDOX) in addition to genes encoding FLS. The results indicate that FeMYBF1 regulates flavonol synthesis and may have a role in synthesis of other flavonoid compounds, and also that buckwheat may have alternative pathway of flavonol synthesis through DFR and LDOX.

Effect of repeated harvesting on the content of caffeic acid and seven species of caffeoylquinic acids in sweet potato leaves.

The purpose of this study was to investigate the effect of repeated harvesting on the content of caffeic acid (CA) and seven species of caffeoylquinic acids (CQAs) in sweet potato leaves using a newly developed high-performance liquid chromatography method. Six cultivars and two breeding lines were used in this study. Leaves were collected at monthly intervals from 1st harvest (May) to 4th harvest (August) in 2011 and 2012. ANOVA analysis revealed that the contents of CQAs were significantly different among all cultivars and breeding lines, but no significant differences were found for CA. No annual variation was confirmed in CA and CQAs. Repeated harvest of sweet potato leaves affected the content of only 4-CQA and 5-CQA. Post-hoc comparisons using Tukey's method indicated that the contents of 4-CQA and 5-CQA in sweet potato leaves harvested at first time were significantly higher compared to those at the other harvest times.

Interspecific pheromone cross-attraction among soybean bugs (Heteroptera): does Piezodorus hybneri (Pentatomidae) utilize the pheromone of Riptortus clavatus (Alydidae) as a kairomone?

The chemical and ecological function of cross-attraction of Piezodorus hybneri (Pentatomidae) to the Riptortus clavatus (Alydidae) pheromone (a mixture of three components) was studied. In a field attraction test using traps with synthetic pheromone components, P. hybneri was attracted to (E)-2-hexenyl (E)-2-hexenoate, a component of the R. clavatus pheromone. Other components had neither an additive nor a synergistic effect on the attraction of P. hybneri. Neither (E)-2-hexenyl (E)-2-hexenoate nor other components of the R. clavatus pheromone were detected in volatiles or whole-body extracts of P. hybneri adults by gas chromatographic analysis. In addition, (E)-2-hexenyl (E)-2-hexenoate could not be found in volatiles of soybean plants. Therefore, it appears that P. hybneri responds to a component of the R. clavatus pheromone that is not emitted by P. hybneri itself. We discuss this interspecific pheromone cross-attraction of the soybean bug and hypothesize that P. hybneri utilizes the pheromone of its competitor as a kairomone for host location.

Polymeric procyanidins as radical-scavenging components in red-hulled rice.

The extracts from white-, black-, and red-hulled rice were prepared by sequential extraction with six different polar solvents, and their radical-scavenging activities were measured by methods using 1,1-diphenyl-2-picrylhydrazyl radical (DPPH*) and tert-butyl hydroperoxyl radical (t-BuOO*). The extracts prepared with highly polar solvents, methanol and deionized water, exhibited higher DPPH* and t-BuOO* scavenging activities in all three cultivars. In addition, the acetone extract from red-hulled rice exhibited a high DPPH* and t-BuOO* scavenging activity, while no such activity was detected for the acetone extracts from white- and black-hulled rice. The major components responsible for the radical scavenging in the acetone extract from red-hulled rice were identified as procyanidins by acidic hydrolysis, vanillin assay, and Sephadex LH-20 chromatography. GPC analysis of the acetylated procyanidins revealed that the average molecular weight is about 5000, in a range of about 500-18,000.

Direct absorption of acylated anthocyanin in purple-fleshed sweet potato into rats.

Absorption of acylated anthocyanins in purple-fleshed sweet potato (Ipomoea batatas cv. Ayamurasaki) in rats was studied to obtain evidence that the acylated anthocyanins themselves could exert a physiological function in vivo. Peonidin 3-caffeoylsophoroside-5-glucoside (Pn 3-Caf*sop-5-glc) in purple-fleshed sweet potato was directly absorbed into rat and present as an intact acylated form in plasma. After oral administration of the purple-fleshed sweet potato anthocyanin (PSA) concentrate containing 38.9 micromol of Pn 3-Caf*sop-5-glc/kg of body weight, Pn 3-Caf*sop-5-glc was detected in the plasma, and the C(max) value and t(max) were estimated as 50.0 +/- 6.8 nmol/Lof plasma and 30 min, respectively. Furthermore, the plasma antioxidant capacity was significantly elevated from 58.0 +/- 12.0 to 89.2 +/- 6.8 micromol of Trolox equivalent/L of plasma 30 min after the administration of the PSA concentrate.