Wide-compatibility Varieties Research Articles

Genetic dissection of embryo sac fertility, pollen fertility, and their contributions to spikelet fertility of intersubspecific hybrids in rice

The partial sterility of hybrids has been a major barrier for utilization of the strong heterosis expressed in hybrids between Oryza sativa ssp. indica and O. sativa ssp. japonica. Wide-compatibility varieties, comprising a special class of germplasm, are able to produce fertile hybrids when crossed to both indica and japonica varieties. However, all the work on wide compatibility and majority of studies on indica/japonica hybrid sterility reported so far were based only on spikelet fertility; thus, it is not known to what extent male and female gamete abortions influence hybrid sterility. In this study, we investigated pollen fertility, embryo sac fertility, and spikelet fertility in an F1 population of 202 true hybrid plants derived from a three-way cross ('02428'/'Nanjing 11'//'Balilla'). A partial regression analysis showed that the pollen and embryo sac fertility contributed almost equally to spikelet fertility. QTL analysis based on a linkage map of 191 polymorphic marker loci identified two QTLs for pollen fertility, one QTL for embryo sac fertility, and three QTLs for spikelet fertility. The S5 locus, previously identified as a locus for wide compatibility by spikelet fertility analysis, is a major locus for embryo sac fertility, and a QTL on chromosome 5 had a major effect on pollen fertility. These two loci coincided with the two major QTLs for spikelet fertility. The study also detected a QTL on chromosome 8, showing a large effect on spikelet fertility but no effect on either pollen or embryo sac fertility. Very little interaction among the QTLs was detected. The implications of the findings in rice breeding programs are discussed.

Identification of Hybrid Sterility Gene Loci in Two Cytoplasmic Male Sterile Lines in Rice

In hybrid rice (Oryza sativa L.) breeding, spikelet sterility is a barrier to attaining enhanced heterosis in crosses between different groups or subspecies of rice. Our objective was to identify the hybrid sterility gene loci (HSGLi) in two indica cytoplasmic male sterile A lines (‘IR58025A’ and ‘IR62829A’) and their corresponding maintainer B lines (‘IR58025B’ and ‘IR62829B’). To detect the HSGL, three testers, ‘IR36’ (indica cultivar), ‘Dular’ (indica wide compatibility variety [WCV]) and ‘Nekken 2’ (japonica WCV) were crossed to the two groups in the form of IR36/WCV//B and A//IR36/WCV. The level of spikelet fertility in the F1 progeny of three-way crosses was differentiated by morphological and isozyme marker genes at the known HSGLi, S5, S7, S8, and S15 on chromosomes 6, 7, 6, and 12, respectively, and by two new HSGLi, on chromosomes 3 and 11. The levels of pollen fertility were differentiated by specific marker alleles among segregating genotypes in the cytoplasmic male sterile (cms) background. The presence of marker alleles from IR36 was associated with high pollen fertility, while marker alleles from Dular and Nekken 2 were associated with low pollen fertility due to the effect of HSGLi in the cms background. The effect of dominant and recessive restorers from IR36 was not estimated due to lack of appropriate markers. To alleviate problems of hybrid sterility, the level of sterility should be tested in crosses between maintainers and restorers before the former are used for backcrossing to create new cms lines.

Identification of segregation-distortion-neutral alleles to improve pollen fertility of indica-japonica hybrids in rice (Oryza sativa L.)

Utilization of the pronounced heterosis of indica-japonica hybrids in rice had been difficult due to panicle sterility caused by male and female gamete abortion in such hybrids. But the female gamete abortion in the most indica-japonicahybrids has been solved by using an abortion-neutral gene S-5 n called as wide compatibility gene. On the other hand, the problem of pollen sterility remains to be solved for such hybrids. This study was conducted to identify abortion-neutral genes for pollen that may be utilized to alleviate pollen sterility in distant crosses. Some cultivars like Ketan Nangka (KN) and Dular, which are known as wide compatibility variety (WCV), were tested to find whether they possess neutral alleles for segregation distortion of marker genes. The distorted segregation of markers as well as normal segregation were confirmed among progeny lines of three-way crosses, WCV/indica//japonica and japonica//indica/WCV. Neutral alleles for segregation distortion were identified at two gamete gene loci (ga), i.e., ga-14(t) on chromosome 3 and ga-11 on chromosome 7. A new locus ga-14(t) was identified in between Pgi-1 and bc-1 and independent of ga-3 on chromosome 3. The neutral alleles at the two loci may be used to solve pollen sterility in indica-japonica hybrids.

The high level of wide-compatibility of variety ‘Dular’ has a complex genetic basis

Wide-compatibility varieties (WCVs) are a special class of rice germplasm that is able to produce fertile hybrids when crossed to both indica and japonica rice varieties. WCVs may differ greatly in their spectrum and level of compatibility. The objective of this study was to determine the genetic basis of wide-compatibility conferred by ‘Dular’, a landrace variety from India that has demonstrated a high level of wide-compatibility in previous studies with a broad range of indica and japonica varieties. A three-way cross (‘Balilla/Dular//Nanjing 11’) was made and the resulting F1 population evaluated in the field for spikelet fertility. A total of 235 plants from this population was assayed individually for restriction fragment length polymorphisms (RFLPs) at 159 marker loci covering the entire rice genome at regular intervals. Quantitative trait locus (QTL) analysis identified 5 loci, located on chromosomes 1, 3, 5, 6 and 8, as having significant effects on hybrid fertility, which jointly explained 55.5% of the fertility variation in this population. The QTL on chromosome 5 ( f5) showed the largest effect on hybrid fertility, followed by those on chromosomes 6 ( f6), 3 ( f3) and 1 ( f1), with the one on chromosome 8 ( f8) having the smallest effect. Genotypes each composed of an allele from ‘Dular’ and an allele from ‘Nanjing 11’ at four ( f3, f5, f6 and f8) of the five QTLs contributed to the increase of fertility in the population. In contrast, the genotype composed of alleles from ‘Balilla’ and ‘Nanjing 11’ at the fifth locus ( f1) was in the direction of increasing fertility. Analysis of variance using marker genotypes at the five QTLs as the groups detected two interactions involving four of the five loci, a 2-locus interaction between f5 and f8 and a 3-locus interaction among f3, f5 and f6. The level of hybrid fertility is the result of complex interactions among these loci. The implication of the present findings in the utilization of the wide-compatibility of ‘Dular’ in rice breeding programs is also discussed.

A genome-wide analysis of wide compatibility in rice and the precise location of the S5 locus in the molecular map

The discovery of wide-compatibility varieties (WCVs) that are able to produce normal fertility hybrids when crossed both to indica and japonica rice has enabled the fertility barrier between indica and japonica subspecies to be broken and provided the possibility of developing inter-subspecific hybrids in rice breeding programs. However, a considerable variation in the fertility level of hybrids from the same WCV crossed to different varieties has often been observed. One hypothesis for this variable fertility is that additional genes are involved in hybrid fertility besides the wide-compatibility gene (WCG). To assess such a possibility, we performed a genome-wide analysis by assaying a large population from a three-way cross ‘02428’/‘Nanjing 11’//‘Balilla’ using a total of 171 RFLP probes detecting 191 polymorphic loci distributed throughout the entire rice linkage map. Our analysis recovered 3 loci conferring significant effects on hybrid fertility. The major locus on chromosome 6 coincided in chromosomal location with the previously identified S 5 locus, and the 2 minor loci that mapped to chromosomes 2 and 12, respectively, were apparently distinct from all previously reported hybrid sterility genes. Interaction between the indica and japonica alleles at each of the loci caused a reduction in hybrid fertility. The joint effect of the 2 minor loci could lead to partial sterility even in the presence of the WCG. The location of the S 5 locus on the molecular marker linkage map was determined to be approximately 1.0 cM from the RFLP locus R2349. This tight linkage will be useful for marker-aided transfer of the WCG in hybrid rice breeding and for map-based cloning.

Molecularmarker diversity and hybrid sterility in indica-japonica rice crosses

The partial sterility of hybrids between the indica and japonica rice subspecies of Asian cultivated rice is a serious constraint for utilizing inter-subspecific heterosis in hybrid rice breeding. In this study, we have investigated the relationship between molecular-marker polymorphism and indica-japonica hybrid fertility using a diallel set involving 20 rice accessions including 9 indica and 11 japonica varieties. Spikelet fertility of the resulting 190 F1s and their parents was examined in a replicated field trial. Intra-subspecific hybrids showed much higher spikelet fertility than inter-subspecific hybrids except in crosses involving wide-compatibility varieties. The parents were surveyed for DNA polymorphism using 96 RFLP and ten SSR markers, which revealed extensive genetic differentiation between indica and japonica varieties. A large number of markers detected highly significant effects on hybrid fertility. The chromosomal locations for many of the positive markers coincided well with previously identified loci for hybrid sterility. The correlation between hybrid fertility and parental distance was low in both intra- and inter-subspecific crosses. The results suggest that the genetic basis of indica-japonica hybrid sterility is complex. It is the qualitative, rather than the quantitative, difference between the parents that determines the fertility of hybrids.

An analysis of hybrid sterility in rice using a diallel cross of 21 parents involving indica, japonica and wide compatibility varieties

There is much interest in the inter-varietal fertility of Asian cultivated rice. In this study, we analyzed the fertility of hybrids in a diallel set of 210 crosses involving 21 parents representing a broad range of the cultivated rice germplasm including landraces, primitive cultivars, modern elite cultivars and parents of hybrid rice. The materials were also carefully selected with respect to indica-japonica classification including typical indica/japonica, more or less intermediate and wide compatibility varieties. The level of hybrid fertility varied widely among the crosses from almost completely sterile to fully fertile. In general, hybrid fertility of intra-subspecific crosses, i.e., indica by indica (I×I) and japonica by japonica (J×J), is much higher than inter-subspecific crosses (I×J or J×I). The fertility varied widely in hybrids involving wide compatibility varieties and also in inter-subspecific crosses not involving wide compatibility varieties. An analysis of variance showed that both the main effects of indica and japonica parents and the interaction between the parents are highly significant in determining hybrid fertility. We speculate that, in addition to wide compatibility, the overall genetic difference between the indica and japonica parents, that may involve a series of minor mutations, play an important role in determining the hybrid fertility. There are also genes of sizable effect that influence fertility in hybrids resulting from specific combinations of the parents.

Studies on Transfer of Bacterial Blight Resistant Genes of Indica-Japonica Crosses inOryzae sativaL

A rice (Oryzae sativa L) indica bacterial blight (BB) resistant variety DV85 was crossed with japonica wide compatibility varieties (WCVs), and results showed that their compatibilities were very poor and the resistant genes in F 2 significantly biased away from normal segregated values by the χ 2 test at the 1% level. This distorted segregation was not related to spikelet fertility, panicle length, grains per panicle and 1000-grain weight by correlation analyses. Four resistant derived lines to BB have been obtained by an anther culture technique. ZD92147 was resistant to Chinese races 1, 3, 4 and Philippine races 1-5 and moderately resistant to Chinese races 2, 5 and Philippine race 6. ZD92152 was resistant to Chinese races 1, 4, Philippine races 1, 2, 3, 5 and moderately resistant to Chinese races 2, 3 and Philippine races 4 and 6. Their resistances equalled or exceeded the level of DV85 and were much better than check variety 'Xiushui 11'. The F 2 of japonica-biased resistant plants of japonica WCVs x DV85 was anther cultured, and results showed that it is a more convenient and effective breeding method than ordinary breeding methods to transfer BB resistant genes in wide crosses. The four derived lines indica-japonica behaviours were also studied. ZD92147 and ZD92149 belong to japonica, ZD92150 belongs to the indica-japonica middle type, while ZD92152 belongs to indica.

Identification of a set of RFLP probes for subspecies differentiation in Oryza sativa L.

Sixty-eight indica-japonica tester-differentiating RFLP probes were tested in seven indica and seven japonica varieties of rice (Oryza sativa L.) with four enzyme digestions (EcoRI, EcoRV, HindIII and DraI). Twenty-one DNA clones were isolated as indica-japonica subspecies-differentiating probes. A set of 13 probes was established as core probes for subspecies differentiation and a pooled blotting analysis was carried out to facilitate the application of RFLP in rice genetics and breeding practice. A dendrogram of 12 wide-compatibility varieties was constructed based on RFLPs detected by 13 core probes with single enzyme digestions. It was speculated that most RFLPs of indica-japonica differentiating probes were generated by insertions/deletions, which may be of great significance for the origin and differentiation of subspecies in Oryza sativa L.

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.

RFLP-based phylogenetic analysis of wide compatibility varieties in Oryza sativa L.

Twenty-one wide compatibility varieties (WCVs) of rice together with three indica and three japonica testers were assayed with 160 DNA probes that were selected to represent the entire RFLP map at an average interval of 11 cM. On the basis of four enzyme digestion 125 probes detected polymorphisms among the WCVs and subspecies' testers. Among these polymorphic probes there were 68 that could distinguish the indica from the japonica testers. Two dendrograms were constructed on the basis of 398 polymorphic fragments of 125 probes and 139 polymorphic fragments of 68 subspecies' differentiating probes in combination with single enzymes, respectively. The reliability and representativeness of the testers and the levels of DNA variations among WCVs were estimated. The potential of WCVs in the utilization of intersubspecific heterosis is discussed.

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.