Molecular mapping of a fertility restorer gene for cytoplasmic male sterility in soybean

In this study, we report the mapping of the Rf locus in soybean by microsatellite simple sequence repeat (SSR) genetic markers. A cross was made between cytoplasmic male sterility (CMS) line JLCMS82A and restorer line JIHUI 1 based on the DNA polymorphisms revealed by 109 SSR markers. A F₂ population derived from a single F₁ plant containing 103 individuals was used for mapping the Rf locus. The Rf gene of JIHUI 1 gametophytically restores male fertility to JLCMS82A. Fertile and semi-fertile DNA bulks and parental DNAs were screened with 219 SSR markers, and Satt215 which was previously mapped to soybean LG J, was found linked to the Rf gene. Five additional polymorphic SSR markers from LG J were used for analysis and a regional linkage map around the Rf locus was established. SSR markers, Sctt011 and Satt547, flanked the Rf locus at 3.6 cM and 5.4 cM, respectively. The availability of these SSR markers will facilitate the selection of restorer lines in hybrid soybean breeding.     

Inheritance and molecular mapping of restorer‐of‐fertility (Rf) gene in A2 hybrid system in pigeonpea (Cajanus cajan)

Inheritance of fertility restorer gene in pigeonpea was studied using F₂ and BC₁F₁ populations derived from cross AL103A × IC245273. It was found to be controlled by single dominant gene. Out of 228 SSR primer pairs, 33 primer pairs showed parental polymorphism, while four primers were found polymorphic in bulk segregant analysis (BSA). These four primers viz., CcM 1615, CcM 0710, CcM 0765 and CcM 1522 were used for genotyping of F₂ population and were found to be placed at 3.1, 5.1, 28.1 and 45.8 cM, respectively. Two of them, CcM 1615 and CcM 0710, evinced clear and unambiguous bands for fertility restoration in F₂ population. The Rf gene was mapped on linkage group 6 between the SSR markers CcM 1615 and CcM 0710 with the distances of 3.1 and 5.1 cM, respectively. The accuracy of the CcM 1615 was validated in 18 restorers and six maintainer lines. The marker CcM 1615 amplified in majority of male restorer lines with a selection accuracy of 91.66%.     

Mapping and genetic analysis of two fertility restorer loci in the wild-abortive cytoplasmic male sterility system of rice (Oryza sativa L.)

Hybrid varieties developed by making use of the wild abortive cytoplasmic male sterility system account for 90% of hybrid rice produced. Previous inheritance studies have established that the fertility restoration in this system is controlled by two major loci, but the chromosomal locations of the fertility restorer (Rf) loci have yet to be resolved. In this study we determined the genomic locations of the two Rf loci by their linkage to molecular markers. The Rf gene containing regions were identified by surveying two bulks, made of 30 highly fertile and 46 highly sterile plants from a large F₂ population of the cross between Zhenshan 97A and Minghui 63, with RFLP markers covering the entire rice genome. The survey identified two likely Rf gene containing regions, located on chromosomes 1 and 10 respectively. This was confirmed by ANOVA using a large random sample from the same F₂ population and also with a genome-wide QTL analysis of a test-cross population. The results also showed that both loci have major effects of almost complete dominance on fertility restoration and the effect of the locus on chromosome 10 is larger than the one on chromosome 1. The two loci acted as a pair of classical duplicate genes; a single dominant allele at one of the two loci would suffice to restore the fertility to normal or nearly normal. Closely linked markers identified in this study may be used for marker assisted selection in hybrid rice breeding programs. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular mapping of a new genic male-sterility gene causing chalky endosperm in rice ( Oryza sativa L.)

A genic male-sterility gene newly induced by chemical mutagenesis, tentatively designated as ms-h(t), was located on the molecular map of rice and tested for its effect on chalky endosperm. Bulked segregant analysis was used to determine the chromosomal location of the ms-h(t) locus by screening four to five RFLP markers per chromosome. After confirming that the gene was located on chromosome 9, twenty-four RFLP markers from chromosome 9 were surveyed for polymorphism in the parents of the mapping population. Of these, eleven markers were mapped around the ms- h(t) locus. RG451 and RZ404 flanked the ms-h(t) gene, at 2.5cM and 3.3cM, respectively. Heterozygous F2 to F4 progenies were tested for co- segregation of male-sterility and chalky endosperm and it was revealed that ms-h(t) might have a pleiotropic effect on chalky endosperm. This mutant would be a good biological material to characterize the biochemical mechanism of male sterility and related pleiotropic effects. Further studies should be needed to know the usefulness of this mutant for hybrid seed production. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular mapping of S-c, an F1 pollen sterility gene in cultivated rice

Hybrids between indica and japonica rice varieties usually show partial sterility, and are a major limiting factor in the utilization of heterosis at subspecific level. When studying male-gamete (pollen) abortion, a possibly important cause for sterility, six loci (S-a, S-b, S-c, S-d, S-e and S-f) for F₁ pollen sterility were identified. Here we report genetic and linkage analysis of S-c locus using molecular markers in a cross between Taichung 65, a japonica variety carrying allele S-c ^j, and its isogenic line TISL5, carrying alleleS-c ^j. Our results show that pollen sterility occurring in the hybrids is controlled by one locus. We used 208 RFLP markers, as well as 500 RAPD primers, to survey the polymorphism between Taichung 65 and TISL5. Six RFLP markers located on a small region of chromosome 3, detected different RFLP patterns. Co-segregation analysis of fertility and RFLP patterns with 123 F₂ plants confirmed that the markers RG227, RG391, R1420 were completely linked with the S-c locus. The genetic distances between the markers C730, RG166 and RG369 and the S-c locus were 0.5 cM, 3.4 cM, and 3.4 cM respectively. Distorted F₂ ratios were also observed for these 4 RFLP markers in the cross. This result suggests that the `one locus sporo-gametophytic' model could explain F₁ hybrid pollen sterility in cultivated rice. RG227, the completely linked marker, has been converted to STS marker for marker-assisted selection. This revised version was published online in August 2006 with corrections to the Cover Date.     

Enhanced grain yield in rice hybrids through complementation of fertility restoration by Rf3 and Rf4 genes as revealed by multilocation evaluation of tropical japonica derived rice (Oryza sativa) hybrids

Thirty-one tropical japonica derived Rf gene carrying rice hybrids were classified into three classes as Rf3, Rf4 and Rf3 + Rf4 hybrids. These hybrids were tested under three different mega-environments. Between Rf3 class and both the classes of hybrids possessing Rf4 genes, significant variation for spikelet and pollen fertility and grain yield was found. The pollen fertility was five times higher among Rf4 hybrids than that of hybrids carrying Rf3 alone. Likewise, spikelet fertility among Rf4 hybrids was two times higher than that of Rf3 hybrids. Parallel grain yield increase in Rf4 hybrids was 2.4 times than in Rf3 hybrids. However, Rf3 gene was found complementing Rf4 to truncate the range of pollen and spikelet fertility. Hybrids possessing Rf3 alone exhibited partial pollen and spikelet sterility, and significant negative standard heterosis for grain yield. The high yielding hybrid, “HYB36” carrying both the Rf genes was found to be widely adapted. The present study established that Rf4 gene is essential either alone or in combination with Rf3 for fertility restoration to achieve enhanced grain yield in WA-CMS based hybrids.     

Fine mapping of Rf2, a major locus controlling pollen fertility restoration in sorghum A1 cytoplasm,encodes a PPR gene and its validation through expression analysis

Sorghum is one of the pioneering cereal crops where cytoplasmic male sterility (CMS) was successfully exploited for mass production of F₁ hybrid seed. Mapping genes for fertility restoration (Rf) is an important aspect of understanding the molecular basis of fertility restoration in crop plants. In this study, we fine‐mapped a fertility restoration locus, Rf2 of sorghum reported earlier (Jordan, Mace, Henzell, Klein, & Klein, 2010 ), involving two F₂ populations (296A × RS29 and 296A × DSV1) and newly developed SSR markers delimited Rf2 locus to 10.32‐kb region on chromosome 2. The Rf2 locus was tightly linked with two new SSRs, MS‐SB02‐3460 (0.14 cM) and MS‐SB02‐3466 (0.75 cM) on both sides, and hosted only one gene (Sobic.002G057050) of PPR gene family. Another new SSR marker developed in the study, MS‐SB02‐37912, forms the part of PPR gene and could act as a perfect marker in marker‐assisted breeding for fertility restoration involving Rf2 in sorghum breeding. The strong involvement of Sobic.002G057050 gene in fertility restoration was supported through RNA expression analysis.     

Inheritance and mapping of a restorer gene for the rapeseed cytoplasmic male sterile line 681A

A novel cytoplasmic male sterility‐fertility restoration system has been developed in rapeseed (Brassica napus). The cytoplasmic male sterile line 681A was derived from a spontaneous male sterile mutant in a newly released double‐low rapeseed cultivar ‘Xiangyou 13′. The restorer line 714R was identified in the interspecific progeny from a B. napus×B. juncea‐cross. Genetic analysis showed that fertility restoration for 681A cytoplasmic male sterility was controlled by a single dominant nuclear gene which might originate from B. juncea. The RAPD marker S1039_‐520 was found to be linked to the restorer gene in F₂ progeny of 681A × 714R with a recombination frequency of 5.45%.     

Genetic mapping for the Rf1 (fertility restoration) gene in sunflower (Helianthus annuus L.) by SSR and TRAP markers

The Rf1 gene in sunflower can effectively restore the pollen fertility of PET1 cytoplasm in male-sterile lines and has been widely used in commercial hybrid production. Identifying molecular markers tightly linked to this gene will be useful in marker-assisted selection to develop maintainer and restorer lines. Rf1 has been mapped to Linkage Group (LG) 13 of the public sunflower simple sequence repeat (SSR) map by aligning maps constructed from different populations and only one SSR marker was reported to be loosely linked to Rf1 . This paper reports the result of applying target region amplification polymorphism (TRAP) and SSR markers to map and develop a sequence-tagged site (STS) marker tightly linked to Rf1 using two populations derived from a cross between two U.S. public sunflower lines, RHA439 and cmsHA441. An SSR marker, ORS511, was 3.7 cM from the Rf1 gene and a TRAP marker, K11F05Sa12-160, was linked to Rf1 at a distance of 0.4 cM. This TRAP marker was converted to an STS marker for using in sunflower breeding.     

Inheritance and mapping of male sterility restoration gene in upland japonica restorer lines

Several upland Japonica breeding lines, WAB450-11-1-3-P40-HB (Abbreviated as WAB450-11), WAB450-11-1-2-P61-HB (WAB450-13), WAB450-l-B-P-91-HB (WAB450-14), IRAT216, IRAT359, and IRAT104, possessing restoring ability for the Dian 1 type cms (cms-D) line Dianyu 1A were recently identified at Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, P. R. China. In this study, the inheritance of restoring ability in these lines was characterized through the production of backcross populations to the male-sterile and maintainer Dianyu 1 lines. Each of the restorer lines was used to pollinate Dianyu 1A to form a F₁ hybrid which was then backcrossed (1) with Dianyu 1B producing a BC₁F₁ population and (2) to the female parent Dianyu 1A producing a BC₅F₂ population. The lines were also crossed with the japonica restorer line C57, carrying the restorer gene Rf1 that was introgressed from indica, to form F₁ hybrids, these hybrids were then testcrossed with Dianyu 1A to study the allelic relationship of their restorer genes to Rf1. The inheritance in these testcross populations indicated that the complete restoring ability of WAB450-11, WAB450-13, WAB450-14, IRAT216, IRAT359, and the partial restoring ability of IRAT104 were controlled by dominant genes, and the gene in WAB450-13, WAB450-14, and IRAT216 was allelic or identical to Rf1. When 136 SSR markers were used to score 143 BC₁F₁ individuals from Dianyu 1A/WAB450-13//Dianyu 1B, the japonica Rf1 allele was found to be located between RM171 and RM6100 on the long arm of chromosome 10, an interval corresponding to that known for the indica Rf1 allele. The distance between RM171 and Rf1 is 2.8 cM, and that between Rf1 and RM6100 is 4.9 cM. Similar linkage results were obtained from mapping 89 individuals of the corresponding BC₅F₂ population (Dianyu 1A/6/Dianyu 1A/WAB450-13).     

Frequency and fertility restoration efficiency of Rf3 and Rf4 genes in Indian rice

Identification of new parental lines is crucial for developing ecology‐specific hybrids with ideal agronomic performance. We screened a total of 570 different ecology‐specific Indian rice varieties for the presence of fertility restorer genes, Rf3 and Rf4 using tightly linked markers DRRM Rf3‐10 and RM6100, respectively. Among these varieties, 13% carried Rf3Rf3/Rf4Rf4, 31% carried rf3rf3/rf4rf4, 6% carried Rf3Rf3/rf4rf4 and remaining 50% carried Rf4Rf4/rf3rf3 allelic combinations. A mini set of 40 varieties with variable allelic combinations of fertility restorer genes were testcrossed with WA and Kalinga‐based CMS lines. All the 80 F₁s were evaluated for spikelet fertility and fertility restoration ability. Rf3Rf3/rf4rf4 genotypes mostly behaved as partial maintainers or partial restorers. In contrast, rf3rf3/Rf4Rf4 genotypes were partial or effective restorers. However, double dominant genotypes showed better fertility restoration than the genotypes containing Rf3 or Rf4 individually. Some of the genotypes showed unexpected restoration pattern implying occurrence of other fertility restorer(s) apart from Rf3 and Rf4. The perfect restorers and maintainers identified in this study can be directly used in hybrid rice breeding.     

A new gene located on chromosome 2 causing hybrid sterility in a remote cross of rice

‘Ketan Nangka’, the donor of the wide compatibility gene (WCG) showed typical hybrid sterility when crossed to a landrace, ‘Bai Mi Fen’, of Yunnan province in China. A genome‐wide analysis was performed for a backcrossed population of ‘Ketan Nangka’/‘Bai Mi Fen’//‘Ketan Nangka’ using a total of 143 simple sequence repeat markers and an expressed sequence tagged marker to cover the entire rice linkage map. As a result, two independent loci were found to cause hybrid sterility via female gamete abortion. The locus on chromosome 4 may correspond to S9, but the other, on chromosome 2, was different from all the previously reported hybrid sterility loci and was designated as S29(t) following the hybrid sterility nomenclature. On the basis of allelic interaction which causes female gamete abortion, two alleles were found: S29^kn(t) in ‘Ketan Nangka’ and S29^bi(t) in ‘Bai Mi Fen’. In the heterozygote, S29^kn(t)/S29^bi(t), which was semi‐sterile, female gametes carrying S29^bi(t) were aborted. An Aus variety from the Indian subcontinent, ‘Dular’, was found to have a neutral allele, S29ⁿ(t). Two molecular markers, RM185 and RM425, linked to S9 and S29(t), respectively, will be useful for marker‐aided transfer of WCGs in hybrid rice breeding.     

Comparison of two fertility restoration systems against photoperiod-sensitive cytoplasmic male sterility in wheat

A ‘two‐line system’ using photoperiod‐sensitive cytoplasmic male sterility (PCMS) caused by Aegilops crassa cytoplasm under a long‐day photoperiod ( 15 h) has been proposed as a new means of producing hybrid varieties in common wheat. The PCMS line is maintained by self‐pollination under short‐day conditions, and hybrid seeds can be produced through outcrossing of the PCMS line with a pollinator under long‐day conditions. Two kinds of fertility restoration systems against the PCMS are known. One is involved with a set of multiple fertility‐restoring (Rf) genes in the wheat cultivar ‘Norin 61’ located on (at least) chromosomes 4A, 1D, 3D and 5D. The other is controlled by a single dominant major Rf gene, Rfd1, located on the long arm of chromosome 7B in the wheat cultivar ‘Chinese Spring’. To examine the degree of fertility restoration by these two systems, nine PCMS lines were crossed with ‘Norin 61’ and ‘Chinese Spring’ as the restorer lines, and the F₁ hybrids were investigated. The degree of fertility restoration was estimated by comparing the seed set rates in the F₁ hybrids having the Ae. crassa cytoplasm and those with normal cytoplasm. The results revealed that the fertility restoration ability of a set of multiple Rf genes in ‘Norin 61’ was higher than that of the Rfd1 gene in ‘Chinese Spring’.     

水稻圆粒基因RS的鉴定和定位

阐明水稻籽粒大小相关基因的遗传和分子机制对水稻产量形成具有重要意义。利用甲基磺酸乙酯(ethyl methanesulfonate, EMS)诱变粳稻品种宁粳3号筛选获得圆粒突变体round seed (rs)。遗传分析表明,突变体rs圆粒表型由单隐性核基因控制。颖壳扫描电镜观察发现,rs籽粒变圆主要是细胞数目改变导致的。在突变体rs中,细胞周期相关基因的表达较野生型显著升高。将RS定位在第3染色体短臂标记RM3413与N3-5之间,物理距离约589 kb。RS突变影响BR信号途径,改变了粒型相关基因的表达。本研究有助于阐明水稻籽粒发育的分子机制。     

QTL mapping and associated marker selection for the efficacy of green plant regeneration in anther culture of rice

Anther culturability of rice is a quantitative trait controlled by nuclear‐encoded genes. The identification of quantitative trait loci (QTL) and associated marker selection for anther culturability is important for increasing the efficiency of green plant regeneration from microspores. QTL associated with the capacity for green plant regeneration in anther culture of rice were mapped on chromosomes 3 and 10 using 164 recombinant inbred (RI) lines from a cross between ‘Milyang 23’ and ‘Gihobyeo’. The quantitative trait locus located on chromosome 10 was detected repeatedly when three anther culture methods were applied and was tightly linked to the markers, RG323, RG241 and RZ400. Associations between these markers and the efficacy of green plant regeneration in 43 rice cultivars and two F₂ populations, ‘MG RI036’/‘Milyang 23’, and ‘MG RI036’;/‘IR 36’ were analysed. One of these markers, RZ400, was able to identify effectively genotypes with good (> 10.0%) and poor (< 3.0%) regenerability, based on the marker genotypes in the cultivars and two F₂ populations. This marker enables the screening of rice germplasm for anther culturability and introgression into elite lines in breeding programmes.     

Genic analysis of hybrid sterility caused by anther indehiscence between distantly related rice varieties

Hybrid sterility of the cross between Silewah, an Indonesian native variety and Hayakogane, a Hokkaido rice variety in Japan was confirmed to be caused by anther indehiscence, based on a lot of spikelets with fewer numbers than 3 of dehiscent anthers and fewer numbers of pollens poured onto stigma per spikelet in Silewah/Hayakogane F1. In Silewah/Hayakogane//Hayakogane BC₁F₁, spikelet fertility was correlated with mean number of dehiscent anthers per spikelet. So, genic analyses for hybrid sterility by anther indehiscence were conducted by scoring spikelet sterility in F₂, BC₁F₁s and triple cross. As a result, it was concluded that the hybrid sterility was controlled by complementary action of three dominant genes. Silewah has one of the three genes and Hayakogane has the other two. It was presumed that the two genes which Hayakogane possesses were derived from those of Aikoku, an old native variety in Japan. This revised version was published online in July 2006 with corrections to the Cover Date.     

Identification of restorers and maintainers for developing basmati and non-basmati hybrids in rice, Oryza sativa

Twenty‐seven improved aromatic lines of germplasm and 18 non‐aromatic disease‐resistant genotypes of rice were test‐crossed with four cytoplasmic male‐sterile lines (IR 58025A, IR 62829A, PMS 3A and PMS 10A). Thirteen aromatic and 10 non‐aromatic genotypes were selected based on pollen fertility, and crosses were repeated to confirm sterility‐maintaining and fertility‐restoring ability. Genotypes were categorized as effective restorers (> 80% spikelet fertility), partial restorers (21‐79% spikelet fertility) and maintainers (< 1% spikelet fertility). The effective basmati restorers identified were Basmati 385, Chandan, P1031‐8‐5‐1, HKR 241‐IET‐12020, SAF Khalsa 7 and Karnal Local. The basmati maintainers identified were Basmati 370, Pusa basmati 1, P615‐K‐167‐13 and P1173‐4‐1. The frequency of restorers obtained was higher for the non‐aromatic than the aromatic basmati type. The performance of restorers varied with cytoplasmic male‐sterile (CMS) line, location and season of testing. The differential ability to restore fertility in the CMS lines that have the wild abortive (WA) cytosterile system could result from different nuclear backgrounds of the CMS lines. These restorers and maintainers possess acceptable grain dimensions, a desirable degree of aroma, volume expansion through linear kernel elongation and cooking quality characteristics of basmati rice. These genotypes will contribute to developing basmati hybrids and provide restorers and maintainers with acceptable key basmati quality characteristics.     

Molecular mapping of a novel blast resistance gene Pi38 in rice using SSLP and AFLP markers

Blast, caused by Magnaporthe grisea, is the most devastating disease of rice worldwide. In this study, the main objective was to identify and map a new gene for blast resistance, in an indica rice cultivar ‘Tadukan’ against blast fungal isolate B157, using molecular tools. F₂ segregating population was derived from ‘CO39’ (susceptible) and ‘Tadukan’ (resistant), and molecular mapping of the blast resistance gene was carried out using simple sequence length polymorphism (SSLP) and amplified fragment length polymorphism (AFLP) methods. Two SSLP markers, RM206 and RM21 and three AFLP markers (AF1: E‐aca/M‐ctt; AF2: E‐aca/M‐cat and AF3: E‐acc/M‐cac2) were identified to be linked to the resistance gene. The co‐segregation analysis using SSLP markers implied that the blast resistance gene designated Pi38 resides on rice chromosome 11.