Masaru Yoshinaga

Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don.

Ipomoea trifida (H. B. K.) G. Don. is the most likely diploid ancestor of the hexaploid sweet potato, I. batatas (L.) Lam. To assist in analysis of the sweet potato genome, de novo whole-genome sequencing was performed with two lines of I. trifida, namely the selfed line Mx23Hm and the highly heterozygous line 0431-1, using the Illumina HiSeq platform. We classified the sequences thus obtained as either ‘core candidates’ (common to the two lines) or ‘line specific’. The total lengths of the assembled sequences of Mx23Hm (ITR_r1.0) was 513 Mb, while that of 0431-1 (ITRk_r1.0) was 712 Mb. Of the assembled sequences, 240 Mb (Mx23Hm) and 353 Mb (0431-1) were classified into core candidate sequences. A total of 62,407 (62.4 Mb) and 109,449 (87.2 Mb) putative genes were identified, respectively, in the genomes of Mx23Hm and 0431-1, of which 11,823 were derived from core sequences of Mx23Hm, while 28,831 were from the core candidate sequence of 0431-1. There were a total of 1,464,173 single-nucleotide polymorphisms and 16,682 copy number variations (CNVs) in the two assembled genomic sequences (under the condition of log2 ratio of >1 and CNV size >1,000 bases). The results presented here are expected to contribute to the progress of genomic and genetic studies of I. trifida, as well as studies of the sweet potato and the genus Ipomoea in general.

Selection of stress-tolerant yeasts for simultaneous saccharification and fermentation (SSF) of very high gravity (VHG) potato mash to ethanol.

Highly concentrated bioethanol production requires less volume in fermentation tanks and conserves distillery energy. We screened osmotolerant yeasts from a collection of 1699 yeast strains at our institute and found that three strains, NFRI3062, NFRI3213, and NFRI3225, were candidates for use in bioethanol production. All of these strains belonged to Saccharomyces cerevisiae. NFRI3062 produced 15.0% (w/v) of ethanol from YPD medium containing 35% glucose cultivated at 30 degrees C for 60 h, while S. cerevisiae NBRC0224, which has previously been reported suitable for ethanol production, only produced 13.0% (w/v). The thermotolerances of NFRI3213 and NFRI3225 were also superior to those of NBRC0224 and NFRI3062. We also demonstrated the simultaneous saccharification and fermentation (SSF) of very high gravity (VHG) potato mash and sweet-potato mash. NFRI3225 produced ethanol from potato mash at the fastest rate and in the highest volume (13.7% (w/v)) among the tested strains. The maximum productivity and ethanol yields were 9.1g/L/h and 92.3%, respectively. Although the potato mash was not sterilized, bacterial contamination was not observed. This may have been due to the growth inhibition of bacteria by the rapid glucose consumption and ethanol production of NFRI3225 during the VHG-SSF process.

Inhibition of the expression of the starch synthase II gene leads to lower pasting temperature in sweetpotato starch

The sweetpotato cultivar Quick Sweet (QS) with a lower pasting temperature of starch is a unique breeding material, but the biochemical background of this property has been unknown. To assess the physiological impact of the reduced isoform II activity of starch synthase (SSII) on the starch properties in sweetpotato storage root, transgenic sweetpotato plants with reduced expressions of the SSII gene were generated and evaluated. All of the starches from transgenic plants showed lower pasting temperatures and breakdown measured by a Rapid Visco Analyzer. The pasting temperatures in transgenic plants were approximately 10–15°C lower than in wild-type plants. Distribution of the amylopectin chain length of the transgenic lines showed marked differences compared to that in wild-type plants: more chains with degree of polymerization (DP) 6–11 and fewer chains with DP 13–25. The starch granules from the storage root of transgenic plants showed cracking on the hilum, while those from wild-type plants appeared to be typical sweetpotato starch. In accordance with these observations, the expression of SSII in the storage roots of the sweetpotato cultivar with low pasting temperature starch (QS) was notably lower than in cultivars with normal starch. Moreover, nucleotide sequence analysis suggested that most of the SSII transcripts in the cultivar with low pasting temperature starch were inactive alleles. These results clearly indicate that the activity of SSII in sweetpotato storage roots, like those in other plants, affects the pasting properties of starch through alteration of the amylopectin structure.

Inheritance of low pasting temperature in sweetpotato starch and the dosage effect of wild-type alleles

Sweetpotato (Ipomoea batatas (L.) Lam.), which is an outcrossing hexaploid, is one of the most important starch-producing crops in the world. During the last decade, new sweetpotato cultivars, e.g. ‘Quick Sweet’, which have approximately 20°C lower pasting temperature, slower retrogradation and higher digestibility of raw starch than ordinary cultivars, have been developed in Japan. Genetic analysis of these variants with low pasting temperature starch was conducted in this study. Using 8 variants and 15 normal clones, 26 families were generated. The results from analyzing these progenies suggested that this trait is a qualitative character controlled by one recessive allele (designated spt), which is inherited in a hexasomic manner. A dosage effect of the wild-type Spt allele was found for starch pasting temperature, although the effect was not linear. These results will aid breeders to develop sweetpotato cultivars with a range of starch pasting temperatures.

Development of AFLP-derived SCAR markers associated with resistance to two races of southern root-knot nematode in sweetpotato

The southern root-knot nematode (SRKN) Meloidogyne incognita severely damages yield and quality in sweetpotato production, and host plant resistance is one of the primary options for SRKN control. Segregation of F1 progeny resistant and susceptible to the SP1 and SP2 races of SRKN suggested that the race-specific resistance of the sweetpotato cultivar “Hi-Starch” is mostly controlled by single genes and that the genes for resistance against each race are closely located. Bulked segregant analysis and subsequent analysis of 86 F1 progeny plants identified nine amplified fragment-length polymorphism markers associated with SRKN resistance and a single linkage map consisting of seven of these markers. Quantitative trait locus (QTL) analysis using the segregating resistance data of the F1 progeny allowed mapping of both a locus with a large effect on resistance to the SRKN race SP1 and another affecting resistance to SP2 to the region around E33M53_090 that was designated as qRmi(t). Two AFLP markers in the vicinity of qRmi(t), E33M53_090 and E41M32_206, were converted to locus-specific sequence-characterized amplified region markers based on their internal and adjacent DNA sequences. These markers might be useful for marker-assisted selection of SRKN resistance in sweetpotato breeding and as a first step to map-based cloning of the responsible QTL(s).

Structural and functional characterization of IbMYB1 genes in recent Japanese purple-fleshed sweetpotato cultivars

To elucidate further the genetic mechanism underlying anthocyanin accumulation in the storage roots of recent Japanese purple-fleshed sweetpotato cultivars, we compared the structure of the IbMYB1 gene in cultivar Ayamurasaki and its spontaneous mutant, AYM96, whose storage roots do not accumulate anthocyanin. Amplification of the IbMYB1 genomic fragment covering the coding sequences suggested that the genome of Ayamurasaki contained three types of IbMYB1 sequences, named IbMYB1-1, IbMYB1-2a and IbMYB1-2b, whereas AYM96 had only IbMYB1-1. Although these three IbMYB1 sequences had identical coding sequences, IbMYB1-1 had a 7-bp insertion in the first intron. IbMYB1-2a and IbMYB1-2b were characterized by a single nucleotide polymorphism in the second intron. Further cloning and sequencing of the flanking regions of these IbMYB1 sequences showed that the promoter and 3′ flanking regions of IbMYB1-2a and IbMYB1-2b were different from those of IbMYB1-1. Genetic analysis using an F1 population derived from a cross between the purple-fleshed cultivar Murasakimasari and AYM96 suggested that IbMYB1-2 sequences are responsible for anthocyanin accumulation in the storage roots. The structural features of these three IbMYB1 sequences and identification of the IbMYB1-2null sequence, which contained sequences very similar to those of the flanking regions of IbMYB1-2a and IbMYB1-2b, but which lacked the sequence around the coding region, suggested that IbMYB1 genes in recent Japanese purple-fleshed cultivars had been established through multiple gene-duplication events.