On the cover

Appearance quality of polished rice grain ripened under low- and high-temperature conditions. Although the appearance quality of ‘Koshihikari’ deteriorates under high-temperature conditions because of increased chalky grain (darkened parts), Apq1-NIL maintains a low rate of chalky grain (This issue, p. 336–342).

(K. Miura: Fukui Prefectural University)

Pre-harvest sprouting (PHS) remains a long-standing problem for the production of barley (Hordeum vulgare) and wheat (Triticum aestivum) worldwide. Grain dormancy, a key trait for the prevention of PHS, controls the timing of germination. Discovery of the causal sequence polymorphisms (CSPs) that produce naturally occurring variation in dormancy will help improve PHS tolerance. The identification of CSPs for dormancy remains difficult, especially for barley and wheat, because they are the last major cereals to have their genomes sequenced. However, recent work has identified several important CSPs that play pivotal roles in fine-tuning the dormancy levels in barley and wheat cultivars. This review summarizes these recent advances, which can be directly applied in breeding programs to improve PHS tolerance. These recent findings indicate the possibility that barley and wheat cultivars grown in East Asia, where much rain falls during the harvest season, will be rich sources of alleles that confer strong dormancy, since these cultivars have been selected to cope with the regional climate. The newly discovered dormant alleles will be useful for improving PHS tolerance around the world, just as Reduced-height (Rht) alleles from Japanese wheat varieties contributed to yield increases for the Green Revolution.

Canopy temperature can be a good indicator of stomatal conductance. To understand the genetic basis of phenotypic differences in stomatal conductance between average and high-yielding rice (Oryza sativa L.) cultivars, we conducted a quantitative trait locus (QTL) analysis of canopy temperature. We developed reciprocal series of backcross inbred lines (BC₁F₆) derived from a cross between the average-yielding japonica cultivar ‘Koshihikari’ and the high-yielding indica cultivar ‘Takanari’. A stable QTL, qCTd11 (QTL for canopy temperature difference on chromosome 11) on the short arm of chromosome 11, accounted for 10.4 and 19.8% of the total phenotypic variance in the two lines; the ‘Takanari’ allele decreased the canopy temperature difference value. A chromosome segment substitution line carrying the Takanari qCTd11 showed a greater reduction in canopy temperature than ‘Koshihikari’, and had higher stomatal conductance and photosynthetic rate. These results suggest that qCTd11 is not only involved in canopy temperature, but is also involved in both stomatal conductance and photosynthetic rate.

Flowering time is an important agronomic trait for Brassica rapa crops, and previous breeding work in Brassica has successfully transmitted other important agronomic traits from donor species. However, there has been no previous attempts to produce hybrids replacing the original Brassica FLC alleles with alien FLC alleles. In this paper, we introduce the creation of a chromosome substitution line (CSSL) containing a homozygous introgression of Flowering Locus C from Brassica oleracea (BoFLC2) into a B. rapa genomic background, and characterize the CSSL line with respect to the parental cultivars. The preferential transmission of alien chromosome inheritance and the pattern of transmission observed during the production of the CSSLs are also discussed.

Branching is a predominant element in the plant architecture of Brassica napus L. and represents an important determinant of seed yield. OsPAT15 (OsDHHC1), a novel DHHC-type zinc finger protein gene, was reported to regulate rice plant architecture by altering the tillering. However, whether heterologous overexpression of the OsPAT15 gene from the monocot rice into the dicot B. napus L. would have the same effect on branching or seed yield is unknown. In this study, the DHHC-type zinc finger protein gene OsPAT15 was determined to have sulfur acyl transferase activity in the akr1Δ yeast mutant in a complementation experiment. Heterologously expressing OsPAT15 transgenic B. napus L. plants were obtained using the Agrobacterium-mediated floral-dip transformation method. As anticipated, OsPAT15 transgenic plants exhibited branching and seed yield. Compared with non-transgenic plants, OsPAT15 transgenic plants had increased primary branches (1.58–1.76-fold) and siliques (1.86–1.89-fold), resulting in a significant increase in seed yield (around 2.39–2.51-fold). Therefore, overexpression of the sulfur acyl transferase gene OsPAT15 in B. napus L. could be used to increase seed yield and produce excellent varieties.

High-temperature stress during the ripening stage leads to quality deterioration due to an increase in chalky grains in brown rice (Oryza sativa L.). In a previous study, we identified a QTL for Appearance quality of brown rice 1 (Apq1) using chromosome segment substitution lines of the indica cultivar ‘Habataki’ in the japonica cultivar ‘Koshihikari’ background and narrowed down the locus to a 48-kb region on chromosome 7. To verify the function and mechanisms of this QTL in grain appearance, in this study, we fine-mapped the gene and conducted high-temperature tolerance tests. As a result of the genetic mapping, we narrowed down the candidate region of Apq1 to a 19.4-kb region including three predicted genes. Among these, the temporal expression pattern of sucrose synthase 3 (Sus3) corresponded well with the high temperature-sensitive period during ripening, and expression of the ‘Habataki’ allele of Sus3 was increased under high-temperature condition. In addition, we transformed the ‘Habataki’ Sus3 gene into ‘Nipponbare’, and the transformants obtained high-temperature tolerance. Therefore, we conclude that the causal gene underlying the QTL Apq1 is the thermo-responsive Sus3 allele, and the increase in Sus3 expression under high-temperature condition during ripening leads to high-temperature tolerance in rice.

Hybrid sterility between Oryza sativa and O. glaberrima is a main reproduction barrier when transferring the favorable alleles from O. glaberrima to O. sativa and it happens due to allelic interaction at sterility loci. Neutral alleles at each locus have the potential to overcome the sterility between the two cultivated rice species. In this study, an O. sativa cultivar Dianjingyou 1 (DJY1) and its near-isogenic lines (NILs) harboring the single sterility allele S1-glab, S19-glab, S20-glab, S37-glab, S38-glab and S39-glab as the tested lines were crossed with O. glaberrima, O. rufipogon, O. nivara, O. glumaepatula, O. barthii, O. meridionalis and O. sativa so as to detect the neutral alleles of these loci. Pollen fertility was investigated in the paired F₁s based on two seasons’ result and genotypic segregation was also analyzed in some F₂ populations to confirm the results of pollen fertility investigation. The neutral alleles of S38-n and S39-n were identified based upon the pollen fertility and genotypic segregation analysis for the first time. The neutral alleles of sterility loci detected from present report have the potential to know of the nature of interspecific hybrid sterility, and to overcome the interspecific hybrid sterility between O. sativa and O. glaberrima.

The timing of flower formation and length of the seed-filling period of indeterminate growth soybean varieties vary more than those of determinate varieties (Glycine max (L.) Merrill). These variations have been hypothesized to affect single seed weight and its uniformity which determine the processing quality of soybean used in foods. We derived near isogenic lines (NILs) with different growth characteristics from an indeterminate line (donor parent) and three determinate lines with heavy seeds (recurrent parents), and evaluated the effects of growth habit on seed weight and its uniformity. Each NIL population consisting of five indeterminate and five determinate BC₄F₄ lines tested at two locations in two different years with two replications. Split-plot analysis of variance, with main-plot and sub-plot being cross combination and growth habit, respectively, showed that indeterminate varieties had slightly heavier seeds than determinate varieties and that there was no significant difference in uniformity of single seed weights. The effects of growth habit on seed uniformity was related to genetic background, but differences between the two growth characteristics were less than the differences among genetic background. This indicates that indeterminate growth habit did not much influence seed weight or its uniformity.

Lilies (Lilium spp.) are one of the most important floricultural crops. As most lily cultivars have originated from interspecific hybridization, they usually have complex genome composition and occasionally fail to develop normal gametes. Further improvement of lily cultivars by sexual crossing requires evaluation of gamete development and subsequent male and female fertility. Although male fertility is easily evaluated through microscopic observation after staining or by pollen culture for germination, evaluation of female fertility is difficult, because gametes develop inside an ovule within an ovary. Lilium species have the Fritillaria type of embryo sac, which, at maturity, consists of a haploid egg apparatus, including one haploid egg cell and two haploid synergids, two polar nuclei (one haploid nucleus and one triploid nucleus) and three triploid antipodal cells. Compared to the Polygonum type of embryo sac, composition of the embryo in the Fritillaria type of embryo sac is complex. We developed an efficient microscopic observation technique for ovules using the clearing procedure, which allowed us to categorize abnormal patterns of female gametes and to elucidate the frequency of abnormal female gamete development. The relationship among normal embryo sac, pollen stainability and seed formation in lily cultivars is discussed.

We present an association analysis for seven key traits related to flowering, stem form and growth in Eucalyptus cladocalyx, a tree species suitable for low rainfall sites, using a long-term progeny trial with 49 open-pollinated maternal families in the southern Atacama Desert, Chile. The progeny trial was carried out in an arid environment with a mean annual rainfall of 152 mm. Simple sequence repeats (SSR) from a full consensus map of Eucalyptus were used for genotyping 245 individual trees. Twenty-three significant marker-trait associations were identified, explaining between 5.9 and 23.7% of the phenotypic variance. The marker EMBRA101 located on LG10 at 56.5 cM was concomitantly associated with diameter at breast height and tree height. Nine SSR were significantly associated with stem forking and stem straightness, explaining between 5.9 and 14.8% of the phenotypic variation. To our knowledge, this is the first study reporting a SSR-based association mapping analysis for stem form traits in Eucalyptus. These results provide novel and valuable information for understanding the genetic base of key traits in E. cladocalyx for breeding purposes under arid conditions.

The genome-wide characterization of single nucleotide polymorphism (SNP) between cultivars or between inbred lines contributes to the creation of genetic markers that are important for plant breeding. Functional markers derived from polymorphisms within genes that affect phenotypic variation are especially valuable in plant breeding. Here, we report on the genome re-sequencing and analysis of the two parental inbred lines of the commercial F₁ hybrid Chinese cabbage cultivar “W77”. Through the genome-wide identification and classification of the SNPs and indels present in each parental line, we identified about 1,500 putative non-functional genes in each parent. We designed cleaved amplified polymorphic sequence (CAPS) markers using specific mutations found at Eco RI restriction sites in the parental lines and confirmed their Mendelian segregation by constructing a linkage map using 96 F₂ plants derived from the F₁ hybrid cultivar, “W77”. Our results and data will be a useful genomic resource for future studies of gene function and metagenomic studies in Chinese cabbage.

To obtain a clear intact section of a ripened rice grain, which is suitable for biochemical and histological analysis, the Kawamoto method using a specific adhesive film was applied using a cryomicrotome. The longitudinal and sagittal sections were easily obtained together with the cross-section, and cell characteristics were clearly discerned in the ripened grain. It was demonstrated that the Kawamoto method is readily applicable for intact sectioning of hard tissue, including ripened grain. Intact section sampling may be useful for enzymatic analysis and transcriptomic analysis of plant tissue.

The oilseed crop Brassica juncea carries many desirable traits; however, resistance to clubroot disease, caused by Plasmodiophora brassicae, is not available in this species. We are the first to report the clubroot resistant resynthesized B. juncea lines, developed through interspecific crosses between a clubroot resistant B. rapa ssp. rapifera and two susceptible B. nigra lines, and the stability of the resistance in self-pollinated generations. The interspecific nature of the resynthesized B. juncea plants was confirmed by using A- and B-genome specific SSR markers, and flow cytometric analysis of nuclear DNA content. Self-pollinated progeny (S₁ and S₂) of the resynthesized B. juncea plants were evaluated for resistance to P. brassicae pathotype 3. The S₁ and S₂ progenies of one of the resynthesized B. juncea lines were resistant to this pathotype. However, resistance was lost in 6 to 13% plants of the S₂ progenies derived from the second resynthesized B. juncea line; this apparently resulted from the loss of the genomic region carrying resistance due to meiotic anomalies.