Fine mapping of S32(t), a new gene causing hybrid embryo sac sterility in a Chinese landrace rice (Oryza sativa L.)

Ketan Nangka, the donor of wide compatibility genes, showed sterility when crossed to Tuanguzao, a landrace rice from Yunnan province, China. Genetic and cytological analyses revealed that the semi-sterility was primarily caused by partial abortion of the embryo sac. Genome-wide analysis of the linkage map constructed from the backcross population of Tuanguzao/Ketan Nangka//Ketan Nangka identified two independent loci responsible for the hybrid sterility located on chromosomes 2 and 5, which explained 18.6 and 20.1% of phenotypic variance, respectively. The gene on chromosome 5 mapped to the previously reported sterility gene S31(t), while the gene on chromosome 2, a new hybrid sterility gene, was tentatively designated as S32(t). The BC₁F₂ was developed for further confirmation and fine mapping of S32(t). The gene S32(t) was precisely mapped to the same region as that detected in the BC₁F₁ but its position was narrowed down to an interval of about 1.9 cM between markers RM236 and RM12475. By assaying the recombinant events in the BC₁F₂, S32(t) was further narrowed down to a 64 kb region on the same PAC clone. Sequence analysis of this fragment revealed seven predicted open reading frames, four of which encoded known proteins and three encoded putative proteins. Further analyses showed that wide-compatibility variety Dular had neutral alleles at loci S31(t) and S32(t) that can overcome the sterilities caused by these two genes. These results are useful for map-based cloning of S32(t) and for marker-assisted transferring of the neutral allele in hybrid 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 F₁ 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 BC₁F₁ 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, F₁ 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 f5-Du, a gene conferring wide-compatibility for pollen fertility in inter-subspecific hybrids of rice (Oryza sativa L.)

Wide-compatibility varieties (WCVs), comprising a special class of rice germplasm, are able to produce fertile hybrids when crossed with both indica and japonica varieties. Dular, a landrace variety from India, has both a wide spectrum and high level of wide-compatibility when crossed with a range of indica and japonica varieties. In previous studies, an allele at the f5 locus from Dular (f5-Du) was identified as a neutral allele conferring wide-compatibility with a large effect on both pollen and spikelet fertility. Using a population of 1993 hybrid plants derived from a cross between ZS(f5-Du/f5-ZS) (F₁ of near isogenic line of Zhenshan 97 containing f5-Du) and Balilla (a japonica tester), f5-Du was genetically mapped to an interval of about 1.6 cM, with 0.8 cM from both SSR markers WFPM3 and WFPR1. Combined with bioinformatic analysis, a contig map was constructed for the f5 region, consisting of five bacterial artificial chromosome (BAC) or P1 artificial chromosome (PAC) clones and spanning approximately 437 kb in length. By assaying the recombinant events in the region with markers developed using the sequence information, the f5 locus was further narrowed down to a 70 kb fragment containing nine predicted genes. The result will be very useful for cloning this gene and marker-assisted transferring of the neutral allele in rice breeding programs.     

Fine mapping of a gene responsible for pollen semi-sterility in hybrids between Oryza sativa L. and O. glaberrima Steud

Asian cultivated rice (Oryza sativa L.) and African cultivated rice (Oryza glaberrima Steud.) are the two main cultivated rice species in the world, with strong heterosis in their F1 hybrids. However, hybrid sterility is a major barrier, although significant heterosis has been observed. In this study, an F1 pollen semi-sterility locus, S19, was identified on rice chromosome 3 by using near-isogenic lines derived from repeated backcross and marker-assisted selection. The typical pollen semi-sterility was observed in F1 hybrids between S19-NIL and Dianjingyou 1. Cytological study of pollen developmental stages indicated that pollen abortion occurred at the late binucleate stage because of a starch accumulation obstacle in some pollen grains. Molecular analysis revealed that the semi-sterility was caused by the abortion of most male gametophytes carrying the S19 allele from the japonica variety Dianjingyou 1. In a population of 12,780 F2 plants derived from S19-NIL/Dianjingyou 1, the S19 locus was fine-mapped to a chromosomal region of 54 kb based on BAC clones of cv. Nipponbare. Interestingly, an addition of a DNA fragment of about 89 kb to the 54-kb region was found in S19-NIL based on BAC clones of O. glaberrima. Gene prediction analysis identified 12 open reading frames (ORF) based on the region of Dianjingyou 1, while 32 ORFs were predicted in S19-NIL. Map-based cloning of this gene will help us to understand the underlying mechanism of hybrid sterility between the two cultivated rice species.     

Genetic and physical mapping of <Emphasis Type="Italic">Pi36</Emphasis>(t), a novel rice blast resistance gene located on rice chromosome 8

Blast resistance in the indica cultivar (cv.) Q61 was inherited as a single dominant gene in two F₂ populations, F₂-1 and F₂-2, derived from crosses between the donor cv. and two susceptible japonica cvs. Aichi Asahi and Lijiangxintuanheigu (LTH), respectively. To rapidly determine the chromosomal location of the resistance (R) gene detected in Q61, random amplified polymorphic DNA (RAPD) analysis was performed in the F₂-1 population using bulked-segregant analysis (BSA) in combination with recessive-class analysis (RCA). One of the three linked markers identified, BA1126₅₅₀, was cloned and sequenced. The R gene locus was roughly mapped on rice chromosome 8 by comparison of the BA1126₅₅₀ sequence with rice sequences in the databases (chromosome landing). To confirm this finding, seven known markers, including four sequence-tagged-site (STS) markers and three simple-sequence repeat (SSR) markers flanking BA1126₅₅₀ on chromosome 8, were subjected to linkage analysis in the two F₂ populations. The locus was mapped to a 5.8 cM interval bounded by RM5647 and RM8018 on the short arm of chromosome 8. This novel R gene is therefore tentatively designated as Pi36(t). For fine mapping of the Pi36(t) locus, five additional markers including one STS marker and four candidate resistance gene (CRG) markers were developed in the target region, based on the genomic sequence of the corresponding region of the reference japonica cv. Nipponbare. The Pi36(t) locus was finally localized to an interval of about 0.6 cM flanked by the markers RM5647 and CRG2, and co-segregated with the markers CRG3 and CRG4. To physically map this locus, the Pi36(t)-linked markers were mapped by electronic hybridization to bacterial artificial chromosome (BAC) or P1 artificial chromosome (PAC) clones of Nipponbare, and a contig map was constructed in silico through Pairwise BLAST analysis. The Pi36(t) locus was physically delimited to an interval of about 17.0 kb, based on the genomic sequence of Nipponbare.     

Pollen semi-sterility1 encodes a kinesin-1-like protein important for male meiosis, anther dehiscence, and fertility in rice

In flowering plants, male meiosis produces four microspores, which develop into pollen grains and are released by anther dehiscence to pollinate female gametophytes. The molecular and cellular mechanisms regulating male meiosis in rice (Oryza sativa) remain poorly understood. Here, we describe a rice pollen semi-sterility1 (pss1) mutant, which displays reduced spikelet fertility (~40%) primarily caused by reduced pollen viability (~50% viable), and defective anther dehiscence. Map-based molecular cloning revealed that PSS1 encodes a kinesin-1-like protein. PSS1 is broadly expressed in various organs, with highest expression in panicles. Furthermore, PSS1 expression is significantly upregulated during anther development and peaks during male meiosis. The PSS1-green fluorescent protein fusion is predominantly localized in the cytoplasm of rice protoplasts. Substitution of a conserved Arg (Arg-289) to His in the PSS1 motor domain nearly abolishes its microtubule-stimulated ATPase activity. Consistent with this, lagging chromosomes and chromosomal bridges were found at anaphase I and anaphase II of male meiosis in the pss1 mutant. Together, our results suggest that PSS1 defines a novel member of the kinesin-1 family essential for male meiotic chromosomal dynamics, male gametogenesis, and anther dehiscence in rice.     

Assessing hybrid sterility in <Emphasis Type="Italic">Oryza glaberrima</Emphasis> × <Emphasis Type="Italic">O. sativa</Emphasis> hybrid progenies by PCR marker analysis and crossing with wide compatibility varieties

Interspecific crossing of the African indigenous rice Oryza glaberrima with Oryza sativa cultivars is hindered by crossing barriers causing 100% spikelet sterility in F₁ hybrids. Since hybrids are partially female fertile, fertility can be restored by back crossing (BC) to a recurrent male parent. Distinct genetic models on spikelet sterility have been developed predicting, e.g., the existence of a gamete eliminator and/or a pollen killer. Linkage of sterility to the waxy starch synthase gene and the chromogen gene C, both located on chromosome 6, have been demonstrated. We selected a segregating BC₂F₃ population of semi-sterile O. glaberrima × O. sativa indica hybrid progenies for analyses with PCR markers located at the respective chromosome-6 region. These analyses revealed that semi-sterile plants were heterozygous for a marker (OSR25) located in the waxy promoter, whereas fertile progenies were homozygous for the O. glaberrima allele. Adjacent markers showed no linkage to spikelet sterility. Semi-sterility of hybrid progenies was maintained at least until the F₄ progeny generation, suggesting the existence of a pollen killer in this plant material. Monitoring of reproductive plant development showed that spikelet sterility was at least partially due to an arrest of pollen development at the microspore stage. In order to address the question whether genes responsible for F₁ sterility in intraspecific hybrids (O. sativa indica × japonica) also cause spikelet sterility in interspecific hybrids, crossings with wide compatibility varieties (WCV) were performed. WCV accessions possess "neutral" S-loci (Sⁿ) improving fertility in intraspecific hybrids. This experiment showed that the tested Sⁿ-loci had no fertility restoring effect in F₁ interspecific hybrids. Pollen development was completely arrested at the microspore stage and grains were never obtained after selfing. This suggests that distinct or additional S-loci are responsible for sterility of O. glaberrima × O. sativa hybrids.Communicated by H.C. Becker     

Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines

 To detect quantitative trait loci (QTLs) controlling seed dormancy, 98 BC₁F₅ lines (backcross inbred lines) derived from a backcross of Nipponbare (japonica)/Kasalath (indica)//Nipponbare were analyzed genetically. We used 245 RFLP markers to construct a framework linkage map. Five putative QTLs affecting seed dormancy were detected on chromosomes 3, 5, 7 (two regions) and 8, respectively. Phenotypic variations explained by each QTL ranged from 6.7% to 22.5% and the five putative QTLs explained about 48% of the total phenotypic variation in the BC₁F₅ lines. Except for those of the QTLs on chromosome 8, the Nipponbare alleles increased the germination rate. Five putative QTLs controlling heading date were detected on chromosomes 2, 3, 4, 6 and 7, respectively. The phenotypic variation explained by each QTL for heading date ranged from 5.7% to 23.4% and the five putative QTLs explained about 52% of the total phenotypic variation. The Nipponbare alleles increased the number of days to heading, except for those of two QTLs on chromosomes 2 and 3. The map location of a putative QTL for heading date coincided with that of a major QTL for seed dormancy on chromosome 3, although two major heading-date QTLs did not coincide with any seed dormancy QTLs detected in this study. Received: 10 October 1997 / Accepted: 12 January 1998     

Identification of the novel recessive gene pi55(t) conferring resistance to Magnaporthe oryzae

The elite rice cultivar Yuejingsimiao 2 (YJ2) is characterized by a high level of grain quality and yield, and resistance against Magnaporthe oryzae. YJ2 showed 100% resistance to four fungal populations collected from Guangdong, Sichuan, Liaoning, and Heilongjiang Provinces, which is a higher frequency than that shown by the well-known resistance (R) gene donor cultivars such as Sanhuangzhan 2 and 28zhan. Segregation analysis for resistance with F₂ and F₄ populations indicated the resistance of YJ2 was controlled by multiple genes that are dominant or recessive. The putative R genes of YJ2 were roughly tagged by SSR markers, located on chromosomes 2, 6, 8, and 12, in a bulked-segregant analysis using genome-wide selected SSR markers with F₄ lines that segregated into 3 resistant (R):1 susceptible (S) or 1R:3S. The recessive R gene on chromosome 8 was further mapped to an interval ≈1.9 cM/152 kb in length by linkage analysis with genomic position-ready markers in the mapping population derived from an F₄ line that segregated into 1R:3S. Given that no major R gene was mapped to this interval, the novel R gene was designated as pi55(t). Out of 26 candidate genes predicted in the region based on the reference genomic sequence of the cultivar Nipponbare, two genes that encode a leucine-rich repeat-containing protein and heavy-metal-associated domain-containing protein, respectively, were suggested as the most likely candidates for pi55(t).     

Identification and fine mapping of <Emphasis Type="Italic">S-d</Emphasis>, a new locus conferring the partial pollen sterility of intersubspecific F<Subscript>1</Subscript> hybrids in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

The partial pollen abortion of hybrids between the indica and japonica subspecies of Asian cultivated rice is one of the major barriers in utilizing intersubspecific heterosis in hybrid rice breeding. Although a single hybrid pollen sterility locus may have little impact on spikelet fertility, the cumulative effect of several loci usually leads to a serious decrease in spikelet fertility. Isolating of the genes conferring hybrid pollen sterility is necessary to understand this phenomenon and to overcome the resulting genetic barrier. In this study, a new locus for F₁ pollen sterility, S-d, was identified on the short arm of chromosome 1 by analyzing the genetic effect of substituted segments of the near-isogenic line E11-5 derived from the japonica variety Taichung 65 (recurrent parent) and the indica variety Dee-geo-woo-gen (donor parent). The S-d locus was first mapped to a 0.8 cM interval between SSR markers PSM46 and PSM80 using a F₂ population of 125 individuals. The flanking markers were then used to identify recombinants from a population of 2,160 plants derived from heterozygotes of the primary F₂ population. Simultaneously, additional markers were developed from genomic sequence divergence in this region. Analysis of the recombinants in the region resulted in the successful mapping of the S-d locus to a 67-kb fragment, containing 17 predicted genes. Positional cloning of this gene will contribute to our understanding of the molecular basis for partial pollen sterility of intersubspecific F₁ hybrids in rice.     

Characterization of two cDNA clones encoding isozymes of the F1F0-ATPase inhibitor protein of rice mitochondria

Two cDNA clones encoding F₁F₀-ATPase inhibitor proteins, which are loosely associated with the F₁ part of the mitochondrial F₁F₀-ATPase, were characterized from rice (Oryza sativa L. cv. Nipponbare). A Northern hybridization showed that the two genes (designated as IF ₁ -1 and IF ₁ -2) are transcribed in all the organs examined. However, the steady-state mRNA levels varied among organs. A comparison of the deduced amino acid sequences of the two IF ₁ genes and the amino acid sequence of the mature IF₁ protein from potato revealed that IF₁-1 and IF₁-2 have N-terminal extensions with features that are characteristic of a mitochondrial targeting signal. To determine the subcellular localization of the gene products, the IF₁-1 or IF₁-2 proteins were fused in frame to the green fluorescent protein (GFP) or the fused GFP-β-glucuronidase, and expressed transiently in onion or dayflower epidermal cells. Localized fluorescence was detected in mitochondria, confirming that the two IF₁ proteins are targeted to mitochondria. Received: 9 July 1999 / Accepted: 17 August 1999     

Pollen irradiation and gene transfer in Capsicum

Summary The aim of the experiment was to study the possibility of facilitating the gene transfer and reducing the number of required backcrosses through pollen irradiation and subsequent selection of F₁M₁ plants containing a very high proportion of sterile pollen as male parent for backcrossing. Anthers of a donor line, C-3-1, were irradiated with 1,500 rad -rays and the pollen used for pollination of a recipient genotype W-8 which posseses a number of recessive marker genes. Five F₁M₂ plants containing more than 80% sterile pollen grains and one semi-sterile plant were selected and used for backcross to W-8. The segregation pattern of four characters expressed in the first backcross generation [W–8×(W–8×C–3–1)] was assessed and compared with the non-irradiated control. A changed segregation pattern was observed (in some cases even non-transfer of a paternal allele) as well as a shift towards more plants possessing the investigated maternal alleles. A scheme for backcross procedure in combination with pollen irradiation is discussed.     

Fine Mapping of <Emphasis Type="Italic">qHD4-1</Emphasis>, a QTL Controlling the Heading Date,to a 20.7-kb DNA Fragment in Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

A library consisting of 1,123 single-segment substitution lines (SSSLs) in the same genetic background of an elite rice variety Huajingxian74 (HJX74) was evaluated for heading date. From this library, the SSSL W05-1-11-5-16-2-5 with the substituted interval of PSM103—RM348-OSR15-PSM382-RM131-RM127—RM280 was found having a gene, which stably performed extreme late heading date which performed stable and late heading in the different environments of Shandong, Guangdong, and Hainan. To map the gene governing heading date, the SSSL W05-1-11-5-16-2-5 was crossed with the recipient HJX74 to develop an F₂ segregating population. The distribution of late and early heading plants in this population fitted a segregation ratio of 3:1, indicating the late heading was controlled by a dominant gene. The gene locus for heading date was tentatively designated as qHD4-1. Using a random sample of 460 individuals from the F₂ segregation population, the qHD4-1 locus was mapped between two SSR markers RM3335 and RM17572, with genetic distances of 0.1 and 0.2 cM, respectively. For fine mapping of qHD4-1, a large F_2:3 segregating population of 3,000 individuals were developed from F₂ plants heterozygous in the RM3335-RM17572 region. Recombinants analyses further mapped qHD4-1 to an interval of 20.7-kb-bounded WB05 and the WB06. Sequence analysis of this 20.7-kb region revealed that it contains three open reading frames (ORFs), encoding wall-associated receptor kinase-like 5, putative F-box domain containing protein, and putative arogenate/prephenate dehydratase. Of them, ORF1, predicting to encode serine/threonine kinase, is considered the most likely as the candidate gene. The genetic and physical map of the qHD4-1 locus will be very useful in molecular cloning of the qHD4-1gene.     

Effect of short-term heat exposure on physiological traits of indica rice at grain-filling stage

Heat stress impacts the quantity and quality of rice grains, particularly during grain-filling stage needed for grain development. In this study, the effect of short heat stress (42 °C, 30 min) on indica rice plants at the grain-filling stage (dough grain stage) was found by determining their physiological and growth traits F_v/F_m, ?F/F_m′, chlorophyll content, leaf water potential (LWP), membrane stability, relative leaf area (RLA), relative plant height (RPH), total grain weight per panicle (TGW) and 1000 GW. Thai economic rice cvs. KDML105 and Pathumthani 1 (PTT1) were compared to the heat-tolerant rice cultivars N22 and Dular and to the heat-sensitive rice cultivar IR64. The results showed that short heat stress exhibited effects on physiology and growth greater than the control (35 °C, 30 min) by reducing of F_v/F_m, ?F/F_m′, chlorophyll content, LWP, membrane stability and RLA. This result impacted the TGW and 1000 GW. A higher reduction of physiological traits was shown in IR64, followed by KDML105. In contrast, N22 and Dular were minimally affected by heat stress and were able to adapt and recover based on their grain weight that exhibited less of an effect. PTT1 was also impacted by heat stress similarly to Dular. Thus, short heat stress affected the physiological parameters of five rice cultivars at the dough grain stage. In addition, the five indica rice cultivars were classified into three groups: (1) the heat-tolerant group (N22, Dular and PTT1), (2) the moderately heat-tolerant group (KDML105), and (3) the heat-sensitive group (IR64) by PC-ORD program at 50% of similarity of the 13 physiological traits.     

Inheritance of two endosperm protein loci in rice (Oryza sativa L.)

Summary Previous studies indicated two types of phenotypic protein markers as two minor bands of SDS-PAGE for rice storage protein. A variant derived from a Pakistani variety, Dular, was found to show a mobility variant with Band 11, a relatively faster-moving band as compared to Band 10, while most of the other cultivated rices exhibited Band 10 at a molecular weight of around 100–110 K. Band 11 was also observed in several wild rice species. How this variant occurred is not known. Another marker is characterized by the presence of either Band 56 (slower-migrating band) or Band 57 (faster-migrating band) in most cultivars at a molecular weight of about 28–27 K. Most indica varieties developed in Taiwan have Band 57 and japonica varieties have Band 56. Genetic analysis of F₁, F₂ and F₃ seeds from interstrain crosses indicated that Band 10 versus Band 11 and Band 56 versus Band 57 are due to codominant alleles at two loci. Tests of independent inheritance between these two loci (Band 10/11 versus Band 56/57) indicated that there is no linkage between them. Both of these two protein loci encode for endosperm proteins and mostly belong to the minor polypeptide subunits of the glutelin fraction of rice seed proteins. Studies on reciprocal crosses indicate dosage effects as exhibited in band patterns. Variations in band intensity were frequently observed when the maternal genotype was different.     

The hybrid protein interactome contributes to rice heterosis as epistatic effects

Heterosis is the phenomenon in which hybrid progeny exhibits superior traits in comparison with those of their parents. Genomic variations between the two parental genomes may generate epistasis interactions, which is one of the genetic hypotheses explaining heterosis. We postulate that protein?protein interactions specific to F₁ hybrids (F₁‐specific PPIs) may occur when two parental genomes combine, as the proteome of each parent may supply novel interacting partners. To test our assumption, an inter‐subspecies hybrid interactome was simulated by in silico PPI prediction between rice japonica (cultivar Nipponbare) and indica (cultivar 9311). Four‐thousand, six‐hundred and twelve F₁‐specific PPIs accounting for 20.5% of total PPIs in the hybrid interactome were found. Genes participating in F₁‐specific PPIs tend to encode metabolic enzymes and are generally localized in genomic regions harboring metabolic gene clusters. To test the genetic effect of F₁‐specific PPIs in heterosis, genomic selection analysis was performed for trait prediction with additive, dominant and epistatic effects separately considered in the model. We found that the removal of single nucleotide polymorphisms associated with F₁‐specific PPIs reduced prediction accuracy when epistatic effects were considered in the model, but no significant changes were observed when additive or dominant effects were considered. In summary, genomic divergence widely dispersed between japonica and indica rice may generate F₁‐specific PPIs, part of which may accumulatively contribute to heterosis according to our computational analysis. These candidate F₁‐specific PPIs, especially for those involved in metabolic biosynthesis pathways, are worthy of experimental validation when large‐scale protein interactome datasets are generated in hybrid rice in the future.     

Putative homozygous mutations in regenerated plants of rice

Summary Both normal and putative homozygous mutant (dwarf mutant) rice plants were regenerated from diploid seed callus, cultured in the presence of 1% NaCl. This trait was transmitted at least through the eighth genration (D₈) of regenerated plants (D₁) by self-pollination, as a homozygous mutation. However, the trait disappeared in the F₁, F₂, F₃ and F₄ obtained by reciprocal crosses of mutant plants with either control plants or with progeny of normal regenerated plants. Chimeric reversion of the homozygous mutant trait was observed and the revertant phenotype was transmitted stably to at least three successive generations. Similar dwarf types of homzygous mutation were observed independently in the two varieties, Norin 8 and Nipponbare, in an experimental series of ca. 3000 D₁ plants. The frequency of mutations among regenerated plants was calculated to be 1.8×10^-2. The mechanism responsible for these phenomena may be heritable gene inactivation induced by in vitro culture.     

Identification of simple sequence repeat markers for utilizing wide-compatibility genes in inter-subspecific hybrids in rice (Oryza sativa L.)

Although pronounced heterosis in inter-subspecific hybrids was known in rice for a long time, its utilization for hybrid rice breeding has been limited due to their hybrid sterility (HS). For the last two decades, however, a few inter-subspecific hybrids have been developed by incorporating wide-compatibility genes (WCG) that resolve HS, into parental lines of these inter-subspecific hybrids. For effective use of WCG, it is necessary to find convenient markers linked to WCG of practical importance. In this paper, initially a set of simple sequence repeat (SSR) markers in the vicinity of known WCG loci identified based on comparative linkage maps have been surveyed in a population derived from the three-way cross- IR36/Dular//Akihikari, where a known donor of WCG Dular was crossed to a representative indica and japonica cultivar. Of the five parental polymorphic markers, RM253 and RM276 were found to be closely linked to the WCG locus S5 at a distance of 3.0 and 2.8 cM, respectively. Later, loci for HS were examined in three F₂ populations derived from inter-subspecific crosses, with same set of SSR markers. The locus S8 was confirmed to have major influence on HS in the F₂ population derived from CHMRF-1/Taichung65 since two SSR markers in its vicinity, RM412 and RM141, co-segregated with HS at a map distance of 7.6 and 4.8 cM, respectively. In the F₂ population derived from the cross BPT5204/Taipei309, three SSR markers in the vicinity of S5, RM50, RM276 and RM136 co-segregated with HS at a map distance of 4.2, 3.2 and 7.8 cM, respectively. In the third F₂ population derived from Swarna/Taipei309, the SSR markers in the vicinity of S5, RM225, RM253, RM50, RM276 and RM136 were identified to co-segregate with HS at a map distance of 3.2, 2.6, 3.4, 2.6 and 6.6 cM, respectively. These results indicated a clear picture of WCG in Dular as well as the predominant role of HS alleles at S5 locus. The identified SSR markers are expected to be used for incorporation of WCG into parental lines in hybrid rice breeding to solve HS in inter-subspecific hybrids.S.P. Singh , R.M. Sundaram contributed equally     

High-resolution genetic mapping of bacterial blight resistance gene <Emphasis Type="Italic">Xa10</Emphasis>

Bacterial blight of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most devastating disease of rice (Oryza sativa L). Rice lines that carry resistance (R) gene Xa10 confer race-specific resistance to Xoo strains harboring avirulence (Avr) gene avrXa10. Here we report on genetic study, disease evaluation and fine genetic mapping of the Xa10 gene. The inheritance of Xa10-mediated resistance to PXO99^A(pHM1avrXa10) did not follow typical Mendelian inheritance for single dominant gene in F₂ population derived from IR24 × IRBB10. A locus might be present in IRBB10 that caused distorted segregation in F₂ population. To eliminate this locus, an F₃ population (F₃-65) was identified, which showed normal Mendelian segregation ratio of 3:1 for resistance and susceptibility. A new near-isogenic line (F₃-65-1743) of Xa10 in IR24 genetic background was developed and designated as IRBB10A. IRBB10A retained similar resistance specificity as that of IRBB10 and provided complete resistance to PXO99^A(pHM1avrXa10) from seedling to adult stages. Linkage analysis using existing RFLP markers and F₂ mapping population mapped the Xa10 locus to the proximal side of E1981S with genetic distance at 0.93 cM. With five new RFLP markers developed from the genomic sequence of Nipponbare, Xa10 was finely mapped at genetic distance of 0.28 cM between proximal marker M491 and distal marker M419 and co-segregated with markers S723 and M604. The physical distance between M491 and M419 on Nipponbare genome is 74 kb. Seven genes have been annotated from this 74-kb region and six of them are possible Xa10 candidates. The results of this study will be useful in Xa10 cloning and marker-assisted breeding.