Geographic distribution of Waxy gene SNPs and indels in foxtail millet, Setaria italica (L.) P. Beauv.

To elucidate diversity and evolution of the Waxy gene in foxtail millet, Setaria italica, we analyzed sequence polymorphism of Waxy gene in 83 foxtail millet landraces collected from various regions covering the entire geographical distribution of this millet in Europe and Asia. We found a unique geographic distribution pattern at the sequence level of gene haplotypes and also found a large diversity in East Asian landraces. We also found a higher degree of genetic polymorphism in a non-waxy phenotype than in other low amylose types, supporting the hypothesis that low amylose types recently originated from non-waxy type.     

Linkage analysis of rice bacterial blight resistance gene xa20 in XM6, a mutant line from IR24

Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is an important disease constraining rice (Oryza sativa L.) production worldwide. The XM6 line was induced by N-methyl-N-nitrosourea from IR24, an Indica cultivar that is susceptible to Philippine and Japanese Xoo races. XM6 was confirmed to carry a recessive gene named xa20, resistant to six Philippine and five Japanese Xoo races. The chromosomal gene location was found using 10 plants with the shortest lesion length in an F₂ population consisting of 298 plants from a susceptible Japonica variety Koshihikari × XM6. Analysis using PCR-based DNA markers covering the whole rice genome indicated the gene as located on the distal region of the long arm of chromosome 3. The IKC3 line carries IR24 genetic background with Koshihikari fragment on chromosome 3 where a resistance gene was thought to be located. The F₂ population from IKC3 × XM6 clearly showed a bimodal distribution separating resistant and susceptible plants. Further linkage analysis conducted using this F₂ population revealed that xa20 is located within the 0.8 cM region flanked by DNA markers KIC3-33.88 (33.0 Mb) and KIC3-34.06 (33.2 Mb). This study yields important findings for resistance breeding and for the genetic mechanism of Xoo resistance.     

Genetic analysis of ion-beam induced extremely late heading mutants in rice

Two extremely late heading mutants were induced by ion beam irradiation in rice cultivar ‘Taichung 65’: KGM26 and KGM27. The F₂ populations from the cross between the two mutants and Taichung 65 showed clear 3 early: 1 late segregation, suggesting control of late heading by a recessive gene. The genes identified in KGM26 and KGM27 were respectively designated as FLT1 and FLT2. The two genes were mapped using the crosses between the two mutants and an Indica cultivar ‘Kasalath’. FLT1 was located on the distal end of the short arm of chromosome 8. FLT2 was located around the centromere of chromosome 9. FLT1 might share the same locus as EHD3 because their chromosomal location is overlapping. FLT2 is inferred to be a new gene because no gene with a comparable effect to that of this gene was mapped near the centromere of chromosome 9. In crosses with Kasalath, homozygotes of late heading mutant genes showed a large variation of days to heading, suggesting that other genes affected late heading mutant genes.     

Chromosomal Location of HWA1 and HWA2, Complementary Hybrid Weakness Genes in Rice

Hybrid weakness phenomena in rice reportedly have two causes: those of HWC1 and HWC2 genes and those of HWA1 and HWA2 genes. No detailed study of the latter has been reported. For this study, we first produced crosses among cultivars carrying the weakness-causing allele on the HWA1 and HWA2 loci to confirm the phenotype of the hybrid weakness and the genotypes of the cultivars on the two loci, as reported earlier. We then confirmed that these cultivars belong to Indica. Subsequent linkage analysis of HWA1 and HWA2 genes conducted using DNA markers revealed that both genes are located in the 1,637-kb region, surrounded by the same DNA markers on the long arm of chromosome 11. The possibility of allelic interaction inducing hybrid weakness is discussed.     

Chromosomal location of Hwc2, one of the complementary hybrid weakness genes, in rice

A hybrid weakness phenomenon is controlled by a set of complementary genes, Hwc1 (hybrid weakness c) and Hwc2, in rice. The Hwc2 gene is prevalent among temperate Japonica but not among tropical Japonica or Indica. In this study, the chromosomal location of the Hwc2 locus was determined from the segregation in the F₁ hybrids made between 127 recombinant inbred lines and the cultivar ‘Jamaica’. Hwc2 was located between the two restriction fragment length polymorphism loci, XNpb264 and XNpb197 on chromosome 4. Further analysis indicated that Hwc2 was closely linked to Ph (phenol staining). The genetic and phylogenetic significance of the Hwc2 locus and the surrounding chromosomal region is discussed.     

Photoperiod insensitivity gene essential to the varieties grown in the northern limit region of paddy rice (Oryza sativa L.) cultivation

Summary The release of extremely early maturing varieties has made it possible to cultivate rice in Hokkaido (NL45-42°) in Japan, the northern limit region of paddy rice cultivation. Until then, rice cultivation in this region has been impracticable due to the climate condition, especially short summer and long-day more than 15 hours during summer. Experiment results confirmed that the success of rice cultivation in this area depends on raising photoperiod insensitivity varieties with short basic vegetative growth period. Moreover, in this study, the genetic factors controlling the photoperiod insensitivity of Hokkaido varieties were analyzed by using 8 kinds of tester lines for three loci, E1, E2, and E3, controlling photoperiod sensitivity. It was found out that all the varieties examined carry el, a photoperiod insensitivity allele of E1 locus, but as for the other loci, E2 and E3, the existence of plural alleles were recognized. We have already clarified that almost all the japonica-type varieties grown in Japan (except Hokkaido) and Taiwan carry E1 bringing about strong photoperiod sensitivity. Accordingly, it can be concluded that el is the gene essential to Hokkaido varieties: the interchange of E1 with e1 enabled rice cultivation under long-day condition.     

Geographical variation of foxtail millet, Setaria italica (L.) P. Beauv. based on rDNA PCR–RFLP

The rDNA PCR–RFLP of foxtail millet (Setaria italica) germ-plasm collected throughout Eurasia and from a part of Africa was investigated with five restriction enzymes according to our previous study. Foxtail millet germ-plasms were classified by length of the rDNA IGS and RFLP; clear geographical differentiation was observed between East Asia, the Nansei Islands of Japan-Taiwan-the Philippines area, South Asia and Afghanistan-Pakistan. We also found evidence of migration of foxtail millet landraces between the areas. We calculated diversity index (D) for each region and found that center of diversity of this millet is East Asia such as China, Korea and Japan.     

Fine Mapping of HWC2, a Complementary Hybrid Weakness Gene, and Haplotype Analysis Around the Locus in Rice

Hybrid weakness is a reproductive barrier. In rice, the hybrid weakness caused by two complementary genes––HWC1 and HWC2––has been surveyed extensively. However, their gene products and the molecular mechanism that causes hybrid weakness have remained unknown. We first performed fine mapping of HWC2, narrowing down the area of interest to 19 kb. We thereby identified five candidate genes. Second, we performed haplotype analysis around the HWC2 locus of 33 cultivars. With 15 DNA markers examined, all the 13 Hwc2-1 carriers share the same haplotype for consecutive 14 DNA markers. As for hwc2-2 carriers, five out of 20 have the haplotypes relatively similar to those of Hwc2-1 carriers. However, the other haplotypes differ remarkably from them. These results are useful to identify the HWC2 gene and to study rice varietal differentiation.     

Genetic analyses of low photoperiod sensitivity of rice cultivars from the northernmost regions of Japan

The genetic factors controlling the extremely low photoperiod sensitivity (PS) of rice culyibstd from the northernmost regions of Japan were studied using 26 cultivars from the Hokkaido district (42 N 45 N). They were grown under 10-h and 24-h daylengths, and their PS. expressed by the difference between the days to heading under these daylengths, was estimated. The genetic factors responsible for the intervarietal difference in PS were then analysed under 10-h, 14-h and 24-h daylengths using the progenies from crosses between Hokkaido cultivars. These results showed that a recessive gene, se-9(t), drastically reduced PS under a 24-h daylength and that several genes, including se9(t), determined the extremely low PS of the cultivars from the northernmost regions.     

rDNA polymorphism of foxtail millet (Setaria italica ssp. italica) landraces in northern Pakistan and Afghanistan and in its wild ancestor (S. italica ssp. viridis)

Ribosomal DNA (rDNA) spacer length polymorphism was studied in foxtail millet (Setaria italica ssp. italica) landraces from Pakistan and Afghanistan and in its wild ancestor (S. italica ssp. viridis) from Pakistan by PCR-based methods. Sequence polymorphism was also investigated for accessions selected based on the observed length polymorphism. The PCR-based length polymorphism and sequence polymorphism of rDNA intergenic spacer (IGS) clearly demonstrated genetic differentiation between cultivated and wild forms in the region. Genetic differentiation was observed between different areas to some extent in the cultivated form, and between different regions in the wild form of northern Pakistan. Based on the results, we discuss the genetic differentiation of foxtail millet and wild ancestor in this region and possible utility of rDNA markers to trace the dispersal of this crop in the region.