Delimitation of the <Emphasis Type="Italic">fgr</Emphasis> gene for rice fragrance to a 28-kb DNA fragment

The fragrance gene plays an important role in high-quality rice varieties and has been widely used in breeding programs. Using a random sample of 370 individuals from an F₂ segregating population developed from a cross between a japonica rice variety 9407 with fragrant flavor and an indica variety IRBB60, the fgr locus was mapped on chromosome 8 between SSR markers, PSM465 and RM1109, with genetic distances of 0.3 cM and 0.1 cM to respective markers. These mapping efforts confirmed the previous mapping results. A large F₃ mapping population with 7300 individuals was then developed from F₂ plants, in which a small chromosomal region defined by the SSR markers, PSM465 and RM1109, was heterozygous. The analysis of recombinants in the fgr region anchored the gene locus to an interval of 28 kb flanked by the left marker NS9 and the right marker L06. Sequence analysis of this fragment predicted three open reading frames encoding putative 3-methylcrotonyl-CoA carboxylase, putative isoleucyl-tRNA synthetase, and betaine aldehyde dehydrogenase (BADH2). The latter was presumed to be the candidate gene for fragrance. This result will be very useful in molecular cloning of the fgr gene and marker-assisted transfer of the fgr gene in rice breeding programs. Published in Russian in Fiziologiya Rastenii, 2009, vol. 56, No. 4, pp. 587–595. This text was submitted by the authors in English.     

Molecular tagging and mapping of the erect panicle gene in rice

Erect panicle (EP) is one of the more important traits of the proposed ideotype of high-yielding rice. Several rice cultivars with the EP phenotype, which has been reported to be controlled by a dominant gene, have been successfully developed and released for commercial production in North China. To analyze the inheritance of the EP trait, we generated segregating F₂ and BC₁F₁ populations by crossing an EP-type variety, Liaojing 5, and a curved-panicle-type variety, Fengjin. Our results confirmed that a dominant gene controls the EP trait. Simple-sequence repeat (SSR) and bulked segregant analyses of the F₂ population revealed that the EP gene is located on chromosome 9, between two newly developed SSR markers, RM5833-11 and RM5686-23, at a genetic distance of 1.5 and 0.9 cM, respectively. Markers closer to the EP gene were developed by amplified fragment length polymorphism (AFLP) analysis with 128 AFLP primer combinations. Three AFLP markers were found to be linked to the EP gene, and the nearest marker, E-TA/M-CTC₂₀₀, was mapped to the same location as SSR marker RM5686-23, 1.5 cM from the EP gene. A local map around the EP gene comprising nine SSR and one AFLP marker was constructed. These markers will be useful for marker-assisted selection (MAS) for the EP trait in rice breeding programs.     

Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line

Low temperature at the booting stage is a serious abiotic stress in rice, and cold tolerance is a complex trait controlled by many quantitative trait loci (QTL). A QTL for cold tolerance at the booting stage in cold-tolerant near-isogenic rice line ZL1929-4 was analyzed. A total of 647 simple sequence repeat (SSR) markers distributed across 12 chromosomes were used to survey for polymorphisms between ZL1929-4 and the cold-sensitive japonica cultivar Towada, and nine were polymorphic. Single marker analysis revealed that markers on chromosome 7 were associated with cold tolerance. By interval mapping using an F₂ population from ZL1929-4 × Towada, a QTL for cold tolerance was detected on the long arm of chromosome 7. The QTL explained 9 and 21% of the phenotypic variances in the F₂ and F₃ generations, respectively. Recombinant plants were screened for two flanking markers, RM182 and RM1132, in an F₂ population with 2,810 plants. Two-step substitution mapping suggested that the QTL was located in a 92-kb interval between markers RI02905 and RM21862. This interval was present in BAC clone AP003804. We designated the QTL as qCTB7 (quantitative trait locus for cold tolerance at the booting stage on chromosome 7), and identified 12 putative candidate genes.     

Fine mapping and candidate gene analysis of <Emphasis Type="Italic">ptgms2-1</Emphasis>, the photoperiod-thermo-sensitive genic male sterile gene in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Photoperiod-thermo-sensitive genic male sterile (PTGMS) rice exhibits a number of desirable traits for hybrid rice production. The cloning genes responsible for PTGMS and those elucidating male sterility mechanisms and reversibility to fertility would be of great significance to provide a foundation to develop new male sterile lines. Guangzhan63S, a PTGMS line, is one of the most widely used indica two-line hybrid rice breeding systems in China. In this study, genetic analysis based on F₂ and BC₁F₂ populations derived from a cross between Guangzhan63S and 1587, determined a single recessive gene controls male sterility in Guangzhan63S. Molecular marker techniques combined with bulked-segregant analysis (BSA) were used and located the target gene (named ptgms2-1) between two SSR markers RM12521 and RM12823. Fine mapping of the ptgms2-1 locus was conducted with 45 new Insertion–Deletion (InDel) markers developed between the RM12521 and RM12823 region, using 634 sterile individuals from F₂ and BC₁F₂ populations. Ptgms2-1 was further mapped to a 50.4 kb DNA fragment between two InDel markers, S2-40 and S2-44, with genetic distances of 0.08 and 0.16 cM, respectively, which cosegregated with S2-43 located on the AP004039 BAC clone. Ten genes were identified in this region based on annotation results from the RiceGAAS system. A nuclear ribonuclease Z gene was identified as the candidate for the ptgms2-1 gene. This result will facilitate cloning the ptgms2-1 gene. The tightly linked markers for the ptgms2-1 gene locus will further provide a useful tool for marker-assisted selection of this gene in rice breeding programs.     

Genetic Analysis and Molecular Mapping of a Novel Gene Conferring Resistance to Rice Stripe Virus

Rice stripe virus (RSV) is one of the most damaging diseases affecting rice in East Asia. Rice variety 502 is highly resistant to RSV, while variety 5112 is extremely susceptible. Field statistical data revealed that all “502 × 5112” F₁ individuals were resistant to RSV and the ratio of resistant to susceptible plants was 3:1 in the F₂ population and 1:1 in the BC₁F₁ population. These results indicated that a dominant gene, designated RSV1, controlled the resistance. Simple sequence repeat (SSR) analysis was subsequently carried out in an F₂ population. Sixty SSR markers evenly distributed on the 12 rice chromosomes were screened and tested. Two markers, RM229 and RM206, showed linkage with RSV1. Based on this result, six SSR markers flanking RM229 and RM206 were further selected and tested. Results indicated that SSR markers RM457 and RM473E were linked to RSV1 with a genetic distance of 4.5 and 5.0 cM, respectively. All of the four SSR markers (RM229, RM473E, RM457 and RM206) linked to RSV1 were all located on chromosome 11, therefore RSV1 should be located on chromosome 11 also. In order to find some new markers more closely linked to the RSV1 gene, sequence-related amplified polymorphism (SRAP) analysis was performed. A total of 30 SRAP primer-pairs were analyzed, and one marker SR1 showed linkage with RSV1 at a genetic distance of 2.9 cM. Finally, RSV1 gene was mapped on chromosome 11 between SSR markers RM457 and SRAP marker SR1 with a genetic distance of 4.5 cM and 2.9 cM, respectively.     

Mapping and Marker-assisted Selection of a Brown Planthopper Resistance Gene bph2 in Rice (Oryza sativa L.)

Nilaparvata lugens Stål (brown planthopper, BPH), is one of the major insect pests of rice (Oryza sativa L.) in the temperate rice-growing region. In this study, ASD7 harboring a BPH resistance gene bph2 was crossed to a susceptible cultivar C418, a japonica restorer line. BPH resistance was evaluated using 134 F_2:3 lines derived from the cross between “ASD7” and “C418”. SSR assay and linkage analysis were carried out to detect bph2. As a result, the resistant gene bph2 in ASD7 was successfully mapped between RM7102 and RM463 on the long arm of chromosome 12, with distances of 7.6 cM and 7.2 cM, respectively. Meanwhile, both phenotypic selection and marker-assisted selection (MAS) were conducted in the BC₁F₁ and BC₂F₁ populations. Selection efficiencies of RM7102 and RM463 were determined to be 89.9% and 91.2%, respectively. It would be very beneficial for BPH resistance improvement by using MAS of this gene.     

Inheritance studies of SSR and ISSR molecular markers and phylogenetic relationship of rice genotypes resistant to tungro virus

Multivariate analyses were performed using 13 morphological traits and 13 molecular markers (10 SSRs and three ISSRs) to assess the phylogenetic relationship among tungro resistant genotypes. For morphological traits, the genotypes were grouped into six clusters, according to D² statistic and Canonical vector analysis. Plant height, days to flowering, days to maturity, panicle length, number of spikelet per panicle, number of unfilled grain per panicle and yield were important contributors to genetic divergence in 14 rice genotypes. Based on Nei's genetic distance for molecular studies, seven clusters were formed among the tungro resistant and susceptible genotypes. Mantel's test revealed a significant correlation (r = 0.834*) between the morphological and molecular data. To develop high yielding tungro resistant varieties based on both morphological and molecular analyses, crosses could be made with susceptible (BR10 and BR11) genotypes with low yielding but highly resistant genotypes, Sonahidemota, Kumragoir, Nakuchimota, Khaiyamota, Khairymota and Kachamota. The chi-square analysis for seven alleles (RM11, RM17, RM20, RM23, RM80, RM108 and RM531) of SSR and five loci (RY1, MR1, MR2, MR4 and GF5) of three ISSR markers in F₂ population of cross, BR11 × Sonahidemota, showed a good fit to the expected segregation ratio (1:2:1) for a single gene model.     

Identification of microsatellite markers for fragrance in rice by analysis of the rice genome sequence

Several chemical constituents are important to the fragrance of cooked rice. However, the chemical compound 2-acetyl-1-pyrroline (AP) is regarded as the most important component of fragrance in the basmati- and jasmine-style fragrant rices. AP is found in all parts of the plant except the roots. It is believed that a single recessive gene is responsible for the production of fragrance in most rice plants. The detection of fragrance can be carried out via sensory or chemical methods, although each has their disadvantages. To overcome these difficulties, we have identified an (AT)₄₀ repeat microsatellite or simple sequence repeat (SSR) marker for fragrant and non-fragrant alleles of the fgr gene. Identification of this marker was facilitated through use of both the publicly available and restricted access sequence information of the Monsanto rice sequence databases. Fifty F₂ individuals from a mapping population were genotyped for the polymorphic marker. This marker has a high polymorphism information content (PIC = 0.9). Other SSR markers linked to fragrance could be identified in the same way of use in other populations. This study demonstrates that analysis of the rice genome sequence is an effective option for identification of markers for use in rice improvement.     

SSRs for Marker-Assisted Selection for Blast Resistance in Rice (Oryza sativa L.)

Rice blast caused by the fungus Magnaporthe oryzae is one of the most devastating diseases of rice in nearly all rice growing areas of the world including Malaysia. To develop cultivars with resistance against different races of M. oryzae, availability of molecular markers along with marker-assisted selection strategies are essential. In this study, 11 polymorphic simple sequence repeat (SSR) markers with good fit of 1:2:1 ratio for single gene model in F₂ population derived from the cross of Pongsu seribu 2 (Resistant) and Mahsuri (Susceptible) rice cultivars were analysed in 296 F₃ families derived from individual F₂ plants to investigate association with Pi gene conferring resistance to M. oryzae pathotype. Parents and progeny were grouped into two phenotypic classes based on their blast reactions. Chi-square test for the segregation of resistance and susceptibility in F₃ generation fitted a ratio of approximately 3:1. Association of SSR markers with phenotypic trait in F₃ families was identified by statistical analysis. Four SSR markers (RM413, RM5961, RM1233 and RM8225) were significantly associated with blast resistance to pathotype 7.2 of M. oryzae in rice (p ≤ 0.01). These four markers accounted for about 20% of total phenotypic variation. So, these markers were confirmed as suitable markers for use in marker-assisted selection and confirmation of blast resistance genes to develop rice cultivars with durable blast resistance in Malaysian rice breeding programmes.     

Usefulness of marker‐assisted selection to improve maize for increased resistance to Sesamia nonagrioides attack with no detrimental effect on yield

Two decades of investigations on maize resistance to Mediterranean corn borer (Sesamia nonagrioides Lefebvre; MCB) have shown that breeding for increased resistance to stem tunnelling by MCB often resulted in reduced yield because significant genetic correlation between both traits exists in some backgrounds. Unlike phenotypic selection, marker‐assisted selection (MAS) could differentiate markers linked only to one trait from those linked simultaneously to yield potential and susceptibility to the pest. In the current study, the suitability of MAS for improving resistance to stem tunnelling without adverse effects on yield has been tested. The unfavourable genetic relationship between yield potential and susceptibility could be overcome using MAS. Gains obtained using MAS were weak, because genetic variance explained by the quantitative trait loci (QTL) was low but results encourage us to persevere in using marker information for simultaneous improvement of resistance and yield especially if genome‐wide approaches are applied. Approaches to detect QTL are widely used, but studies on the suitability of markers linked to QTL for performing MAS have been mostly neglected.     

Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis

An F_4:5 population of 490 recombinant inbred lines (RILs) from the cross Apo/^2*Swarna was used to detect quantitative trait loci (QTL) with large effects on grain yield under drought stress using bulk-segregant analysis (BSA). Swarna is an important rainfed lowland rice variety grown on millions of hectares in Asia, but is highly susceptible to drought and aerobic soil conditions. Apo is an aerobic-adapted variety with moderate tolerance to drought. Two rice microsatellite (RM) markers, RM324, and RM416, located on chromosomes 2 and 3, respectively, were shown via BSA to be strongly associated with yield under lowland drought stress. The effects of these QTL were tested in a total of eight hydrological environments over a period of 3 years. The QTL linked to RM416 (DTY _3.1 ) had a large effect on grain yield under severe lowland drought stress, explaining about 31% of genetic variance for the trait (P < 0.0001). It also explained considerable variance for yield under mild stress in lowland conditions and aerobic environments. To our knowledge this is the first reported QTL that has a large effect on yield in both lowland drought and aerobic environments. The QTL linked to RM324 (DTY _2.1 ) had a highly significant effect on grain yield in lowland drought stress (R ² = 13–16%) and in two aerobic trials. The effect of these QTL on grain yield was verified to be not mainly due to phenology differences. Effects of DTY _3.1 on yield under stress have been observed in several other rice mapping populations studied at IRRI. Results of this study indicate that BSA is an effective method of identifying QTL alleles with large effects on rice yield under severe drought stress. The Apo alleles for these large-effect QTL for grain yield under drought and aerobic conditions may be immediately exploited in marker-assisted-breeding to improve the drought tolerance of Swarna.     

Fine Mapping QTL for Drought Resistance Traits in Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) Using Bulk Segregant Analysis

Drought stress is a major limitation to rice (Oryza sativa L.) yields and its stability, especially in rainfed conditions. Developing rice cultivars with inherent capacity to withstand drought stress would improve rainfed rice production. Mapping quantitative trait loci (QTLs) linked to drought resistance traits will help to develop rice cultivars suitable for water-limited environments through molecular marker-assisted selection (MAS) strategy. However, QTL mapping is usually carried out by genotyping large number of progenies, which is labour-intensive, time-consuming and cost-ineffective. Bulk segregant analysis (BSA) serves as an affordable strategy for mapping large effect QTLs by genotyping only the extreme phenotypes instead of the entire mapping population. We have previously mapped a QTL linked to leaf rolling and leaf drying in recombinant inbred (RI) lines derived from two locally adapted indica rice ecotypes viz., IR20/Nootripathu using BSA. Fine mapping the QTL will facilitate its application in MAS. BSA was done by bulking DNA of 10 drought-resistant and 12 drought-sensitive RI lines. Out of 343 rice microsatellites markers genotyped, RM8085 co-segregated among the RI lines constituting the respective bulks. RM8085 was mapped in the middle of the QTL region on chromosome 1 previously identified in these RI lines thus reducing the QTL interval from 7.9 to 3.8 cM. Further, the study showed that the region, RM212–RM302–RM8085–RM3825 on chromosome 1, harbours large effect QTLs for drought-resistance traits across several genetic backgrounds in rice. Thus, the QTL may be useful for drought resistance improvement in rice through MAS and map-based cloning.     

High-resolution mapping of <Emphasis Type="Italic">Rsn1</Emphasis>, a locus controlling sensitivity of rice to a necrosis-inducing phytotoxin from <Emphasis Type="Italic">Rhizoctonia solani</Emphasis> AG1-IA

Rhizoctonia solani is a necrotrophic fungal pathogen that causes disease on many crop-plant species. Anastomosis group 1-IA is the causal agent of sheath blight of rice (Oryza sativa L.), one of the most important rice diseases worldwide. R. solani AG1-IA produces a necrosis-inducing phytotoxin and rice cultivar’s sensitivity to the toxin correlates with disease susceptibility. Unlike genetic analyses of sheath blight resistance where resistance loci have been reported as quantitative trait loci, phytotoxin sensitivity is inherited as a Mendelian trait that permits high-resolution mapping of the sensitivity genes. An F₂ mapping population derived from parent cultivars ‘Cypress’ (toxin sensitive) and ‘Jasmine 85’ (toxin insensitive) was used to map Rsn1, the necrosis-inducing locus. Initial mapping based on 176 F₂ progeny and 69 simple sequence repeat (SSR) markers located Rsn1 on the long arm of chromosome 7, with tight linkage to SSR marker RM418. A high-resolution genetic map of the region was subsequently developed using a total of 1,043 F₂ progeny, and Rsn1 was mapped to a 0.7 cM interval flanked by markers NM590 and RM418. Analysis of the corresponding 29 Kb genomic sequences from reference cultivars ‘Nipponbare’ and ‘93-11’ revealed the presence of four putative genes within the interval. Two are expressed cytokinin-O-glucosyltransferases, which fit an apoptotic pathway model of toxin activity, and are individually being investigated further as potential candidates for Rsn1.     

Novel Y‐chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations

Y‐chromosome markers are important tools for studying male‐specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non‐human mammals is often hampered by the lack of Y‐specific polymorphic markers. We identified new male‐specific short tandem repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5–10 alleles per locus), falling in one duplicated and two single‐copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five domestic pig populations. European wild boar were characterized by significantly higher levels of haplotype diversity compared to European domestic pigs (H_D = 0.904 ± 0.011 and H_D = 0.491 ± 0.077 respectively). Relationships among STR haplotypes were investigated by combining them with single nucleotide polymorphisms at two linked genes (AMELY and UTY) in a network analysis. A differentiation between wild and domestic populations was observed (F_ST = 0.229), with commercial breeds sharing no Y haplotype with the sampled wild boar. Similarly, a certain degree of geographic differentiation was observed across Europe, with a number of local private haplotypes and high diversity in northern populations. The described Y‐chromosome markers can be useful to track male inheritance and gene flow in wild and domestic populations, promising to provide insights into evolutionary and population genetics in Sus scrofa.     

Screening of IR50?×?Rathu Heenati F7 RILs and Identification of SSR Markers Linked to Brown Planthopper (Nilaparvata lugens St?l) Resistance in Rice (Oryza sativa L.)

Brown planthopper (Nilaparvata lugens St?l) is one of the major insect pests of rice. A Sri Lankan indica rice cultivar Rathu Heenati was found to be resistant to all biotypes of the brown planthopper. In the present study, a total of 268 F₇ RILs of IR50 and Rathu Heenati were phenotyped for their level of resistance against BPH by the standard seedbox screening test (SSST) in the greenhouse. A total of 53 SSR primers mapped on the chromosome 3 were used to screen the polymorphism between the parents IR50 and Rathu Heenati, out of which eleven were found to be polymorphic between IR50 and Rathu Heenati. The eleven primers that have shown polymorphism between the IR50 and Rathu Heenati parents were genotyped in a set of five resistant RILs and five susceptible RILs along with the parents for co-segregation analysis. Among the eleven primers, two primers namely RM3180 (18.22 Mb) and RM2453 (20.19 Mb) showed complete co-segregation with resistance. The identification of SSR markers linked with BPH resistant could be used for the maker assisted selection (MAS) program in rice breeding and to map the resistant genes on rice chromosomes for further gene cloning.     

The use and abuse of genetic marker‐based estimates of relatedness and inbreeding

Genetic marker‐based estimators remain a popular tool for measuring relatedness (r_xy) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of r_xy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker‐based estimators of r_xy and F in a species with very low genetic diversity, New Zealand's little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of r_xy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated r_xy or F is relatively high (Pearson's r = 0.66–0.72 and 0.81–0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker‐based estimates of r_xy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator's performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of r_xy and F debatable.     

High‐density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe

Miscanthus is a perennial C₄ grass that has recently become an important bioenergy crop. The efficiency of breeding improved Miscanthus biomass cultivars could be greatly increased by marker‐assisted selection. Thus, a high‐density genetic map is critical to Miscanthus improvement. In this study, a mapping population of 261 F₁ progeny was developed from a cross between two diploid M. sinensis cultivars, ‘Strictus’ and ‘Kaskade’. High‐density genetic maps for the two parents were produced with 3044 newly developed single nucleotide polymorphisms (SNPs) obtained from restriction site‐associated DNA sequencing, and 138 previously mapped GoldenGate SNPs. The female parent (‘Strictus’) map spanned 1599 cM, with 1989 SNPs on 19 linkage groups, and an average intermarker spacing of 0.8 cM. The length of the male parent (‘Kaskade’) map was 1612 cM, with 1821 SNPs, and an average intermarker spacing of 0.9 cM. The utility of the map was confirmed by locating quantitative trait loci (QTL) for the zebra‐striped trait, which was segregating in this population. Three QTL for zebra‐striped presence/absence (zb1, zb2 on LG 7, and zb3 on LG 10) and three for zebra‐striped intensity (zbi1, zbi2, zbi3 on LGs 7, 10, 3) were identified. Each allele that caused striping was recessive. Incomplete penetrance was observed for each zb QTL, but penetrance was greatest when two or more zb QTL were homozygous for the causative alleles. Similarly, the intensity of striping was greatest when two or more zbi QTL were homozygous for alleles that conferred the trait. Comparative mapping indicated putative correspondence between zb3 and/or zbi2 on LG 10 to previously sequenced genes conferring zebra stripe in maize and rice. These results demonstrate that the new map is useful for identifying marker–trait associations. The mapped markers will become a valuable community resource, facilitating comparisons among studies and the breeding of Miscanthus.     

Development of 28 EST‐SSR markers based on transcriptome sequences of Gobiobotia filifer and cross‐species amplification

Gobiobotia filifer is a small benthic fish distributed in Yangtze River Basin. The abundance of G. filifer increased after impoundment of Xiluodu Dam and Xiangjiaba Dam. The state of population structure and changes of genetic diversity before and after impoundment of Xiluodu Dam and Xiangjiaba Dam were interesting issues. However, efficient molecular markers were rare, which will limit us to solve above problems. Twenty‐eight expressed sequence tag SSRs (EST‐SSRs) were successfully identified and verified as stable amplification and polymorphic loci by polyacrylamide gel electrophoresis (PAGE) and capillary electrophoresis. The number of alleles at these EST‐SSR loci ranged from 3 to 14, the polymorphism information content values were 0.125–0.897, and the observed and expected heterozygosities were 0.0–0.857 and 0.132–0.928, respectively. Cross‐species amplification of the 28 loci developed in this study was examined in seven individuals of each of the 7 taxa. The amplification efficiency of 28 EST‐SSRs primer pairs is related to the distance of genetic relationship between cross‐species with G. filifer, and same subfamily species (Xenophysogobio boulengeri and Xenophysogobio nudicorpa) showed the highest (50%) amplification efficiency. These EST‐SSR markers could be used to analyse genetic diversity and population structure of G. filifer and related species.     

High‐resolution insight into recombination events at the SD1 locus in rice

Recombination during meiosis plays an important role in genome evolution by reshuffling existing genetic variations into fresh combinations with the possibility of recovery of lost ancestral genotypes. While crossover (CO) events have been well studied, gene conversion events (GCs), which represent non‐reciprocal information transfer between chromosomes, are poorly documented and difficult to detect due to their relatively small converted tract size. Here, we document these GC events and their phenotypic effects at an important locus in rice containing the SD1 gene, where multiple defective alleles contributed to the semi‐dwarf phenotype of rice in the ‘Green Revolution’ of the 1960s. Here, physical separation of two defects allows recombination to generate the wild‐type SD1 gene, for which plant height can then be used as a reporter. By screening 18 000 F₂ progeny from a cross between two semi‐dwarf cultivars that carry these different defective alleles, we detected 24 GC events, indicating a conversion rate of ~3.3 × 10^?4 per marker per generation in a single meiotic cycle in rice. Furthermore, our data show that indels and single‐nucleotide polymorphisms (SNPs) do not differ significantly in GC rates, at least at the SD1 locus. Our results provide strong evidence that GC by itself can regain an ancestral phenotype that was lost through mutation. This GC detection approach is likely to be broadly applicable to natural or artificial alleles of other phenotype‐related functional genes, which are abundant in other plant genomes.