Molecular analysis of an additional case of hybrid sterility in rice (Oryza sativa L.)

Hybrid sterility hinders the exploitation of the heterosis displayed by japonica × indica rice hybrids. The variation in pollen semi-sterility observed among hybrids between the japonica recipient cultivar and each of two sets of chromosome segment substitution lines involving introgression from an indica cultivar was due to a factor on chromosome 5 known to harbor the gene S24. S24 was fine mapped to a 42 kb segment by analyzing a large F(2) population bred from the cross S24-NIL × Asominori, while the semi-sterility shown by the F(1) hybrid was ascribable to mitotic failure at the early bicellular pollen stage. Interestingly, two other pollen sterility genes (f5-Du and Sb) map to the same region (Li et al. in Chin Sci Bull 51:675-680, 2006; Wang et al. in Theor Appl Genet 112:382-387, 2006), allowing a search for candidate genes in the 6.4 kb overlap between the three genes. By sequencing the overlapped fragment in wild rice, indica cultivars and japonica cultivars, a protein ankyrin-3 encoded by the ORF2 was identified as the molecular base for S24. A cultivar Dular was found to have a hybrid-sterility-neutral allele, S24-n, in which an insertion of 30 bp was confirmed. Thus, it was possible to add one more case of molecular bases for the hybrid sterility. No gamete abortion is caused on heterozygous maternal genotype with an impaired sequence from the hybrid-sterility-neutral genotype. This result will be useful in understanding of wide compatibility in rice breeding.

Fine mapping of a gene causing hybrid pollen sterility between Yunnan weedy rice and cultivated rice (Oryza sativa L.) and phylogenetic analysis of Yunnan weedy rice

Weedy rice represents an important resource for rice improvement. The F(1) hybrid between the japonica wide compatibility rice cultivar 02428 and a weedy rice accession from Yunnan province (SW China) suffered from pollen sterility. Pollen abortion in the hybrid occurred at the early bicellular pollen stage, as a result of mitotic failure in the microspore, although the tapetum developed normally. Genetic mapping in a BC(1)F(1) population (02428//Yunnan weedy rice (YWR)/02428) showed that a major QTL for hybrid pollen sterility (qPS-1) was present on chromosome 1. qPS-1 was fine-mapped to a 110 kb region known to contain the hybrid pollen sterility gene Sa, making it likely that qPS-1 is either identical to, or allelic with Sa. Interestingly, F(1) hybrid indicated that Dular and IR36 were assumed to carry the sterility-neutral allele, Sa ( n ). Re-sequencing SaM and SaF, the two component genes present at Sa, suggested that variation for IR36 and Dular may be responsible for the loss of male sterility, and the qPS-1 sequence might be derived from wild rice or indica cultivars. A phylogenetic analysis based on microsatellite genotyping suggested that the YWR accession is more closely related to wild rice and indica type cultivars than to japonica types. Thus it is probable that the YWR accession evolved from a spontaneous hybrid between wild rice and an ancient cultivated strain of domesticated rice.

Fine mapping of S31, a gene responsible for hybrid embryo-sac abortion in rice (Oryza sativa L.)

Partial abortion of female gametes and the resulting semi-sterility of indica x japonica inter-subspecific rice hybrids have been ascribed to an allelic interaction, which can be avoided by the use of wide compatibility varieties. To further understand the genetic mechanism of hybrid sterility, we have constructed two sets of hybrids, using as male parent either the typical japonica variety Asominori, or the wide compatibility variety 02428; and as female, a set of 66 chromosome segment substitution lines in which various chromosomal segments from the indica variety IR24 have been introduced into a common genetic background of Asominori. Spikelet semi-sterility was observed in hybrid between CSSL34 and Asominori, which is known to carry the sterility gene S31 (Zhao et al. in Euphytica 151:331-337, 2006). Cytological analysis revealed that the semi-sterility of the CSSL34 x Asominori hybrid was caused primarily by partial abortion of the embryo sac at the stage of the mitosis of the functional megaspore. A population of 1,630 progeny of the three-way cross (CSSL34 x 02428) x Asominori was developed to map S31. Based on the physical location of linked molecular markers, S31 was thereby delimited to a 54-kb region on rice chromsome 5. This fragment contains eight predicted open reading frames, four of which encode known proteins and four putative proteins. These results are relevant to the map-based cloning of S31, and the development of marker-assisted transfer of non-sterility allele inducing alleles to breeding germplasm, to allow for a more efficient exploitation of heterosis in hybrid rice.

[QTL analysis of low-temperature-sensitive pollen sterility in Indica-japonica hybrid rice (Oryza sativa L.)]

There existed a number of biological constraints in exploiting the heterosis of indica-japonica hybrid rice. The low-temperature-sensitive sterility (LTSS) of indica-japonica hybrid has become one of the major problems in indica-japonica hybrid rice breeding after the solution of poor fertility of the hybrids by the finding of wide-compatibility gene. Previous studies revealed that the LTSS might be caused by low-temperature-sensitive pollen sterility (LTSPS). However, the genetic basis of LTSPS remained unclear. To explore the genetic basis of LTSPS in indica-japonica hybrid rice, an F2 genetic population derived from 3037 (indica) and 02428 (japonica) was developed. At the booting stage, pollen fertility of F2 population together with parents were surveyed after the treatment with low temperature daily average of 21-23 degrees C. The linkage map was constructed containing 108 SSR markers distributed throughout the whole 12 chromosomes with average marker interval of 16.26 cM. Using software MapMaker/QTL, two putative QTLs, namely qLTSPS2 and qLTSPS5 on chromosomes 2 and 5 were detected by interval mapping, which could explain the phenotypic variation 15.6% and 11.9% respectively. The additive effects were 0.021 and 0.045, dominant effects were -0.246 and -0.215, and the degrees of dominance were 11.7 and 4.8, respectively for the two QTLs. Therefore, the mode of gene action in response to low-temperature stress was overdominance and LTSPS was mainly the result of interaction between the indica and japonica alleles within each locus. In addition, two-way ANOVA showed that the two QTLs acted essentially independent of each other in conditioning LTSPS.

Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza

Large variation in genome size as determined by the nuclear DNA content and the mitotic chromosome size among diploid rice species is revealed using flow cytometry and image analyses. Both the total chromosomal length (r = 0.939) and the total chromosomal area (r = 0.927) correlated well with the nuclear DNA content. Among all the species examined, Oryza australiensis (E genome) and O. brachyantha (F genome), respectively, were the largest and smallest in genome size. O. sativa (A genome) involving all the cultivated species showed the intermediate genome size between them. The distribution patterns of genome-specific repetitive DNA sequences were physically determined using fluorescence in situ hybridization (FISH). O. brachyantha had limited sites of the repetitive DNA sequences specific to the F genome. O. australiensis showed overall amplification of genome-specific DNA sequences throughout the chromosomes. The amplification of the repetitive DNA sequences causes the variation in the chromosome morphology and thus the genome size among diploid species in the genus Oryza.

Self-incompatibility (S) alleles of the Rosaceae encode members of a distinct class of the T2/S ribonuclease superfamily

Stylar ribonucleases (RNases) are associated with gametophytic self-incompatibility in two plant families, the Solanaceae and the Rosaceae. The self-incompatibility-associated RNases (S-RNases) of both the Solanaceae and the Rosaceae were recently reported to belong to the T2 RNase gene family, based on the presence of two well-conserved sequence motifs. Here, the cloning and characterization of S-RNase genes from two species of Rosaceae, apple (Malus x domestica) and Japanese pear (Pyrus serotina) is described and these sequences are compared with those of other T2-type RNases. The S-RNases of apple specifically accumulated in styles following maturation of the flower bud. Two cDNA clones for S-RNases from apple, and PCR clones encoding a further two apple S-RNases as well as two Japanese pear S-RNases were isolated and sequenced. The deduced amino acid sequences of the rosaceous S-RNases contained two conserved regions characteristic of the T2/S-type RNases. The sequences showed a high degree of diversity, with similarities ranging from 60.4% to 69.2%. Interestingly, some interspecific sequence similarities were higher than those within a species, possibly indicating that diversification of S-RNase alleles predated speciation in the Rosaceae. A phylogenetic tree of members of the T2/S-RNase superfamily in plants was obtained. The rosaceous S-RNases formed a new lineage in the tree that was distinct from those of the solanaceous S-RNases and the S-like RNases. The findings suggested that self-incompatibility mechanisms in Rosaceae and Solanaceae are similar but arose independently in the course of evolution.

Two new loci for hybrid sterility in cultivated rice (Oryza sativa L.)

Female gamete abortion in Indica-Japonica crosses of rice was earlier identified to be due to an allelic interaction at the S-5 locus on chromosome 6. Recently, in other crosses of rice, similar allelic interactions were found at loci designated as S-7 and S-8, located on chromosomes 7 and 6 respectively. All of them are independent of each other. At the S-5 locus, Indica and Japonica rice have S-5 (i) and S-5 (j) alleles respectively and Javanicas, such as Ketan Nangka, have a neutral allele S-5 (n) .The S-5 (i) /S-5 (j) genotype is semi-sterile due to partial abortion of female gametes carrying S-5 (j) , but both the S-5 (n) /S-5 (i) and S-5 (n) /S-5 (j) genotypes are fertile. The S-5 (n) allele is thus a "wide-compatibility gene" (WCG), and parents homozygous for this allele are called wide-compatible varieties (WCV). Such parents when crossed with Indica or Japonica varieties do not show F1 hybrid sterility. Wide-compatible parents have been used to overcome sterility barriers in crosses between Indica and Japonica rice. However, a Javanica variety, Ketan Nangka (WCV), showed typical hybrid sterility when crossed to the Indian varieties N22 and Jaya. Further, Dular, another WCV from India, showed typical hybrid sterility when crossed to an IRRI line, IR2061-628-1-6-4-3(IR2061-628). By genetic analyses using isozyme markers, a new locus causing hybrid sterility in crosses between Ketan Nangka and the Indicas was located near isozyme loci Est-1 and Mal-1 on chromosome 4, and was designated as S-9. Another new locus for hybrid sterility in the crosses between Dular and the IR2061-628 was identified and was found linked to four isozyme loci, Sdh-1, Pox-2, Acp-1 and Acp-2, on chromosome 12. It was designated as S-15. On the basis of allelic interactions causing female-gamete abortion, two alleles were found at S-9, S-9 (kn) in Ketan Nangka and S-9 (i) in N22 and Jaya. In the heterozygote, S-9 (kn) /S-9 (i) , which was semisterile, female gametes carrying S-9 (kn) were aborted. The hybrid of Dular and IR2061-628, with a genetic constitution of S-15 (Du) /S-15 (i) , was semi-sterile and the female gametes carrying S-15 (Du) were aborted. A Japonica tester variety, Akihikari, and an Indica variety, IR36, were found to have neutral alleles, S-9 nand S-15 n, at these loci, in addition to S-7 nand at S-7. The accumulation of three neutral alleles into a breeding line should help solve the hybrid sterility problem in wide crosses of rice.

Molecular analysis of the inheritance of the S-5 locus, conferring wide compatibility in Indica/Japonica hybrids of rice (O. sativa L.)

RFLP analysis was conducted on a population derived from a three-way cross to determine the location of the hybrid sterility locus, S-5, in relation to mapped molecular markers and to identify markers that would be useful for selection in breeding. S-5 is of interest to rice breeders because it is associated with spikelet sterility of F1 hybrids in Indica/Japonica crosses. Identification of an S-5 allele which confers fertility in Indica/Japonica hybrids when introgressed into either the Indica or the Japonica parent has been reported. Varieties carrying this S-5 (n) allele are known as "wide compatibility varieties (WCV)". Our data suggests that RFLP marker RG213 on chromosome 6 is closely linked to the S-5 locus and can be efficiently used to identify wide compatibility (WC) lines. RG213 is a single-copy genomic clone that detects three bands of different molecular weights in DNA from Japonica ('Akihikari') and Indica ('IR36') varieties and WC line ('Nekken 2'). We demonstrate that the three alleles detected by this marker could be used to trace the inheritance of the "wide compatible" phenotype in breeders' material.

Identification of self-incompatibility-related glycoproteins in styles of apple (Malus x domestica)

In this study, stylar proteins of apple (Malus x domestica) which correlate with known intervarietal incompatibility relationships and have similar characteristics to the S-glycoproteins of Japanese pear (Pyrus serotina) were surveyed by two-dimensional gel electrophoresis (2D-PAGE). Varietal differences were detected in a group of glycoproteins having Mrs and pIs similar to those of the S-glycoproteins of Japanese pear. 2D-PAGE profiles of these glycoproteins were correlated with intervarietal incompatibility relationships. These glycoproteins reacted with antiserum raised against the S (4)-glycoprotein of Japanese pear, a result suggesting that they may be the products of S-alleles in styles of apple. On the basis of the profiles of the putative S-glycoproteins, S-genotypes were proposed for each of the apple cultivars examined.

Genetic analysis of stunted growth by nuclear-cytoplasmic interaction in interspecific hybrids of Capsicum by using RAPD markers

When eight cultivars of Capsicum annuum were used as female parents in interspecific crosses with two accessions of C. chinense, dwarfism occurred in hybrids originating from 10 out of 16 combinations, while hybrids of the remaining 6 combinations grew normally. In contrast, when C. chinense was used as female parent, all of the hybrids showed severely stunted growth as if affected by a virus. These results suggested that the stunted growth expressed in the cross of C. chinense x C. annuum is caused by an interaction between nuclear gene(s) from C. annuum and the cytoplasm of C. chinense. To examine the number of nuclear gene(s) which cause(s) the stunted growth, we backcrossed F1 hybrids of C. annuum x C. chinense to C. chinense. About one-quarter of the progeny in the backcrossed hybrids of C. chinense x (C. annuum x C. chinense) showed the same stunted growth shown by the f1 hybrids of C. chinense x C. annuum, suggesting that two complementary genes of C. annuum cause the stunted growth. However, the higher abortion rates of ovules and lower germination percentage of seeds in C. chinense x C. annuum than in the selfed C. chinense implied that the genetic ratio of the stunted type would have been higher than that observed in the C. chinense x (C. annuum x C. chinense) progeny. We then attempted a linkage analysis between the stunted growth and randomly amplified polymorphic DNA (RAPD) of C. chinense x (C. annuum x C. chinense) progeny. A RAPD marker that associated with 94% of the stunted plants but not with 94% of the normal one was identified. This confirmed that a single nuclear gene of C. annuum which is linked to the RAPD marker with a recombination value of 6% causes the stunted growth in an interaction with the cytoplasm of C. chinense.

Identification and characterization of stylar glycoproteins associated with self-incompatibility genes of Japanese pear, Pyrus serotina Rehd

Japanese pear (Pyrus serotina Rehd.) exhibits gametophytic self-incompatibility. Following our previous findings that basic ribonucleases in the styles of Japanese pear are associated with self-incompatibility genes (S-RNases), stylar proteins with high pI values were analyzed by two-dimensional gel electrophoresis further to characterize S-RNases. A group of basic proteins of about 30 kDa associated with self-incompatibility genes were identified. These proteins contained sugar chains which reacted with concanavalin A and wheat germ agglutinin, and thus were designated as S-glycoproteins of Japanese pear. The fact that the S-glycoprotein was expressed at a much lower level in a self-compatible mutant than in the original variety suggested a role of S-glycoproteins in mediating self-incompatibility of Japanese pear. Immunoblot analysis indicated that S-glycoproteins are identical to previously identified S-RNases. The S-glycoproteins were predominantly expressed in the style, in the ovary in trace amounts, and not in leaf, pollen or germinated pollen. The N-terminal amino acid sequences of the S-glycoproteins showed homology not only with each other but also with those of the S-allele-associated proteins from plants of the family Solanaceae at levels of about 30-50%.

Segregation distortion via male gametes in hybrids between Indica and Japonica or wide-compatibility varieties of rice (Oryza sativa L)

One or two marker genes on each of chromosomes 3, 4, 6, 7, 8, 11 and 12 of the 12 rice chromosomes were tested for segregation distortion in indica-japonica hybrids. Marker genes on chromosomes 3, 7, 8, 11 and 12 showed clear segregation distortion. This distortion was not related to the proportion of normal pollen. The germinability of the pollen was less than 10% in the hybrids, although 45-55% of the pollen grains appeared to be morphologically normal. The frequent occurrence of segregation distortion and the low germinability of the pollen grains suggested that a large portion of the pollen produced by the Indica-Japonica hybrids was not functional. The fact that the segregation distortion of the same marker may be positive or negative depending on the cross combination suggested the existence of multiple alleles, including distortion-neutral alleles. The latter mitigate pollen sterility in certain hybrid combinations.