Segregation Distortion Loci Research Articles

Unveiling the Genetic Basis Underlying Rice Anther Culturability via Segregation Distortion Analysis in Doubled Haploid Population.

Anther culture (AC) is a valuable technique in rice breeding. However, the genetic mechanisms underlying anther culturability remain elusive, which has hindered its widespread adoption in rice breeding programs. During AC, microspores carrying favorable alleles for AC are selectively regenerated, leading to segregation distortion (SD) of chromosomal regions linked to these alleles in the doubled haploid (DH) population. Using the AC method, a DH population was generated from the japonica hybrid rice Shenyou 26. A genetic map consisting of 470 SNPs was constructed using this DH population, and SD analysis was performed at both the single- and two-locus levels to dissect the genetic basis underlying anther culturability. Five segregation distortion loci (SDLs) potentially linked to anther culturability were identified. Among these, SDL5 exhibited an overrepresentation of alleles from the female parent, while SDL1.1, SDL1.2, SDL2, and SDL7 displayed an overrepresentation of alleles from the male parent. Furthermore, six pairs of epistatic interactions (EPIs) that influenced two-locus SDs in the DH population were discovered. A cluster of genetic loci, associated with EPI-1, EPI-3, EPI-4, and EPI-5, overlapped with SDL1.1, indicating that the SDL1.1 locus may play a role in regulating anther culturability via both additive and epistatic mechanisms. These findings provide valuable insights into the genetic control of anther culturability in rice and lay the foundation for future research focused on identifying the causal genes associated with anther culturability.

Genome-wide dissection of segregation distortion using multiple inter-subspecific crosses in rice.

Mendelian inheritance can ensure equal segregation of alleles from parents to offspring, which provides fundamental basis for genetics and molecular biology. Segregation distortion (SD) leads to preferential transmission of certain alleles from generation to generation. Such violation of Mendelian genetic principle is often accompanied by reproductive isolation and eventually speciation. Although SD is observed in a wide range of species from plants to animals, genome-wide dissection of such biased transmission of gametes is rare. Using nine inter-subspecific rice crosses, a genome-wide screen for SD loci is performed, which reveals 61 single-locus quantitative trait loci and 194 digenic interactions showing distorted transmission ratio, among which 24 new SD loci are identified. Biased transmission of alleles is observed in all nine crosses, suggesting that SD exists extensively in rice populations. 72.13% distorted regions are repeatedly detected in multiple populations, and the most prevalent SD hotspot that observed in eight populations is mapped to chromosome 3. Xian alleles are transmitted at higher frequencies than geng alleles in inter-subspecific crosses, which change the genetic composition of the rice populations. Epistatic interaction contributes significantly to the deviation of Mendelian segregation at the whole-genome level in rice, which is distinct from that in animals. These results provide an extensive archive for investigating the genetic basis of SD in rice, which have significant implications in understanding the reproductive isolation and formation of inter-subspecific barriers during the evolution.

Mapping QTLs using a novel source of salinity tolerance from Hasawi and their interaction with environments in rice

BackgroundSalinity is one of the most severe and widespread abiotic stresses that affect rice production. The identification of major-effect quantitative trait loci (QTLs) for traits related to salinity tolerance and understanding of QTL × environment interactions (QEIs) can help in more precise and faster development of salinity-tolerant rice varieties through marker-assisted breeding. Recombinant inbred lines (RILs) derived from IR29/Hasawi (a novel source of salinity) were screened for salinity tolerance in the IRRI phytotron in the Philippines (E1) and in two other diverse environments in Senegal (E2) and Tanzania (E3). QTLs were mapped for traits related to salinity tolerance at the seedling stage.ResultsThe RILs were genotyped using 194 polymorphic SNPs (single nucleotide polymorphisms). After removing segregation distortion markers (SDM), a total of 145 and 135 SNPs were used to construct a genetic linkage map with a length of 1655 and 1662 cM, with an average marker density of 11.4 cM in E1 and 12.3 cM in E2 and E3, respectively. A total of 34 QTLs were identified on 10 chromosomes for five traits using ICIM-ADD and segregation distortion locus (SDL) mapping (IM-ADD) under salinity stress across environments. Eight major genomic regions on chromosome 1 between 170 and 175 cM (qSES1.3, qSES1.4, qSL1.2, qSL1.3, qRL1.1, qRL1.2, qFWsht1.2, qDWsht1.2), chromosome 4 at 32 cM (qSES4.1, qFWsht4.2, qDWsht4.2), chromosome 6 at 115 cM (qFWsht6.1, qDWsht6.1), chromosome 8 at 105 cM (qFWsht8.1, qDWsht8.1), and chromosome 12 at 78 cM (qFWsht12.1, qDWsht12.1) have co-localized QTLs for the multiple traits that might be governing seedling stage salinity tolerance through multiple traits in different phenotyping environments, thus suggesting these as hot spots for tolerance of salinity. Forty-nine and 30 significant pair-wise epistatic interactions were detected between QTL-linked and QTL-unlinked regions using single-environment and multi-environment analyses.ConclusionsThe identification of genomic regions for salinity tolerance in the RILs showed that Hasawi possesses alleles that are novel for salinity tolerance. The common regions for the multiple QTLs across environments as co-localized regions on chromosomes 1, 4, 6, 8, and 12 could be due to linkage or pleiotropic effect, which might be helpful for multiple QTL introgression for marker-assisted breeding programs to improve the salinity tolerance of adaptive and popular but otherwise salinity-sensitive rice varieties.

Influence of epistatic segregation distortion loci on genetic marker linkages in Japanese flounder

For genetic linkage analysis of Japanese flounder, 160 doubled haploids (DH) were artificially produced using mitotic gynogenesis and were genotyped for 458 simple sequence repeat (SSR) markers, 101 of which show distortional segregation. The genetic linkage map was constructed by modifying recombination fractions between the distorted markers. Between the corrected and uncorrected genetic maps, there were considerable differences in genetic distance, but not in relative locations among markers. Using a liability model, a segregation distortion locus (SDL), with an additive genetic effect of 1.772, was mapped between markers BDHYP387 and Poli56TUF of chromosome 24 in the corrected genetic map. Additionally, six pairs of epistatic SDLs were identified on chromosomes 1, 5, 8, 9, 23, and 24. Changes in genetic distances between markers did not occur on chromosome regions with main effect SDLs. However, most chromosome regions where genetic distances changed covered the detected epistatic SDLs. This study concluded that epistatic SDLs decrease linkages between markers and lengthen genetic distances in Japanese flounder. This finding has been partially validated in other DH populations derived from three female Japanese flounders.

QTL mapping for haploid male fertility by a segregation distortion method and fine mapping of a key QTL qhmf4 in maize.

Four QTL related to haploid male fertility were detected by a segregation distortion method and the key QTL qhmf4 was fine mapped to an interval of ~800kb. Doubled haploid (DH) technology enables rapid development of homozygous lines in maize breeding programs. However, haploid genome doubling is a bottleneck for the commercialization of DH technology and is limited by haploid male fertility (HMF). This is the first study reporting the quantitative trait locus (QTL) analysis of HMF in maize. Four QTL, qhmf1, qhmf2, qhmf3, and qhmf4, controlling HMF have been identified by segregation distortion (SD) loci detection in the selected haploid population derived from 'Yu87-1/Zheng58'. Three loci, qhmf1, qhmf2, and qhmf4, were also detected in the selected haploid population derived from '4F1/Zheng58'. The QTL qhmf4 showed the strongest SD in both haploid populations. Based on the sequence information of 'Yu87-1' and 'Zheng58', thirteen markers being polymorphic between the two lines were developed to saturate the qhmf4 region. A total of 8168 H1BC2 (haploid backcross generation) plants produced from 'Yu87-1' and 'Zheng58' were screened for recombinants. All the 48 recombinants were backcrossed to 'Zheng58' to develop H1BC3 progeny. The heterozygous H1BC3 individuals were crossed with CAU5 to induce haploids. In each H1BC3 progeny, haploids were genotyped and evaluated for anther emergence score (AES). Significant (or no significant) difference (P < 0.05) between haploids with or without 'Yu87-1' donor segment indicated presence or absence of qhmf4 in the donor segment. The analysis of the 48 recombinants narrowed the qhmf4 locus down to an ~800kb interval flanked by markers IND166 and IND1668.

Identification and Characterization of Segregation Distortion Loci on Cotton Chromosome 18.

Segregation distortion is commonly detected via genetic mapping and this phenomenon has been reported in many species. However, the genetic causes of the segregation distortion regions in a majority of species are still unclear. To genetically dissect the SD on chromosome 18 in cotton, eight reciprocal backcross populations and two F2 populations were developed. Eleven segregation distortion loci (SDL) were detected in these ten populations. Comparative analyses among populations revealed that SDL18.1 and SDL18.9 were consistent with male gametic competition; whereas SDL18.4 and SDL18.11 reflected female gametic selection. Similarly, other SDL could reflect zygotic selection. The surprising finding was that SDL18.8 was detected in all populations, and the direction was skewed towards heterozygotes. Consequently, zygotic selection or heterosis could represent the underlying genetic mechanism for SDL18.8. Among developed introgression lines, SDL18.8 was introgressed as a heterozygote, further substantiating that a heterozygote state was preferred under competition. Six out of 11 SDL on chromosome 18 were dependent on the cytoplasmic environment. These results indicated that different SDL showed varying responses to the cytoplasmic environment. Overall, the results provided a novel strategy to analyze the molecular mechanisms, which could be further exploited in cotton interspecific breeding programs.

Characterization of a Segregation Distortion Locus with Powdery Mildew Resistance in a Wheat-Thinopyrum intermedium Introgression Line WE99.

Exploitation of host resistance is important for controlling powdery mildew of wheat (Triticum aestivum L.). In this study, a wheat-Thinopyrum intermedium introgression line, designated WE99, conferred seedling resistance to 47 of 49 Blumeria graminis f. sp. tritici isolates. Genetic analysis demonstrated that the resistance segregation deviated significantly from a single gene Mendelian ratio. However, marker analysis indicated that only a single recessive resistance gene, temporarily designated PmWE99, conferred powdery mildew resistance (Pm). PmWE99 was mapped to chromosome arm 2BS and linked to the three simple-sequence repeat markers Gwm148, Gwm271, and Barc55. Using race spectrum analysis, PmWE99 was shown to be significantly different from the documented genes Pm42 and MlIW170 located on chromosome arm 2BS and, thus, appeared to be a new Pm gene. Examination of the genotype frequencies in the F2:3 families showed that a genetic variation in the PmWE99 interval that favored the transmission of the WE99 allele could be the cause of the deviated segregation. Further investigation revealed that the abnormal segregation only occurred at the PmWE99 interval and was not common at other loci in this population. Identification of PmWE99 will increase the diversity of the Pm genes for wheat improvement.

A high-density SSR genetic map constructed from a F2 population of Gossypium hirsutum and Gossypium darwinii

The cultivated allotetraploid species Gossypium hirsutum, accounts for 90% of the world cotton production, has narrow genetic basis that's why its yield, quality or stress resistance breeding is stagnant. It is therefore, essential to explore desirable genes from Gossypium darwinii which has enviable traits such as high fiber fineness, drought tolerance, fusarium and verticillium resistance. We used G. darwinii as primary plant materials in this study not only to enrich the genetic diversity of exiting germplasm but also to better understand its genome structure. An interspecific high density linkage map of allotetraploid cotton was constructed using F2 population (G. hirsutum×G. darwinii). The map was based entirely on genome-wide simple sequence repeat (SSR) markers. A total of 2763 markers were mapped in 26 linkage groups (chromosomes) covering a genome length of 4176.7cM with an average inter-locus distance of 1.5cM. The length of the chromosomes ranged from 84.7 to 238.5cM with an average length of 160.6cM. At subgenome length was 2160.7cM with an average distance of 1.6cM, where as Dt genome length was 2016cM with an average distance of 1.4cM. There were 601 distorted SSR loci. Less number of segregation distortion loci were located in At subgenome than in Dt subgenome. Two post-polyploidization reciprocal translocations of “A2/A3 and A4/A5” were suggested by 44 pairs of duplicate loci.

Genetic Map Construction and Detection of Genetic Loci Underlying Segregation Distortion in an Intraspecific Cross of Populus deltoides.

Based on a two-way pseudo-testcross strategy, high density and complete coverage linkage maps were constructed for the maternal and paternal parents of an intraspecific F2 pedigree of Populus deltoides. A total of 1,107 testcross markers were obtained, and the mapping population consisted of 376 progeny. Among these markers, 597 were from the mother, and were assigned into 19 linkage groups, spanning a total genetic distance of 1,940.3 cM. The remaining 519 markers were from the father, and were also were mapped into 19 linkage groups, covering 2,496.3 cM. The genome coverage of both maps was estimated as greater than 99.9% at 20 cM per marker, and the numbers of linkage groups of both maps were in accordance with the 19 haploid chromosomes in Populus. Marker segregation distortion was observed in large contiguous blocks on some of the linkage groups. Subsequently, we mapped the segregation distortion loci in this mapping pedigree. Altogether, eight segregation distortion loci with significant logarithm of odds supports were detected. Segregation distortion indicated the uneven transmission of the alternate alleles from the mapping parents. The corresponding genome regions might contain deleterious genes or be associated with hybridization incompatibility. In addition to the detection of segregation distortion loci, the established genetic maps will serve as a basic resource for mapping genetic loci controlling traits of interest in future studies.

QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight functionalities are integrated in this software package: (1) BIN: binning of redundant markers; (2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci; (5) BIP: mapping of additive, dominant, and digenic epistasis genes; (6) MET: QTL-by-environment interaction analysis; (7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.

Identification of quantitative trait loci for bolting and flowering times in Chinese kale (Brassica oleracea var. alboglabra) based on SSR and SRAP markers

SUMMARYExpressed sequence tag-simple sequence repeat (EST-SSR), simple sequence repeat (SSR), and sequence-related amplified polymorphism (SRAP) markers were used to construct the first intra-specific genetic linkage map for B. oleracea var. alboglabra. In addition, QTL locations were determined for bolting and flowering traits. A total of 189 polymorphic marker loci were detected in the two parents, with 45 marker loci not located on any linkage group (LG). The remaining 144 loci defined ten LGs and included 69 EST-SSR loci, three SSR loci, and 72 SRAP loci. The length of the map was 1,173.8 cM, the average distance between loci was 8.15 cM, and the proportion of segregation distortion loci was 25.7%. Three QTLs controlling bolting time and two QTLs controlling flowering time were detected in the F2:3 generation, which explained 37.07% and 18.44% of the phenotypic variation, respectively. Two QTLs controlling bolting time and two QTLs controlling flowering time were detected in the F2 generation, which explained 27.90% and 25.59% of the phenotypic variation, respectively. In both generations, QTLs ftB.1 and ftA.1 were located on LG5, and the distance between the two QTLs was only 1.0 cM, suggesting that they could be at an identical locus. These results provide a useful reference for future QTL studies on bolting and flowering time in B. oleracea var. alboglabra, and can be used to identify markers linked to these QTLs for marker-assisted selection in commercial breeding programmes.

Linkage group correction using epistatic distorted markers in F2 and backcross populations.

Epistasis has been frequently observed in all types of mapping populations. However, relatively little is known about the effect of epistatic distorted markers on linkage group construction. In this study, a new approach was proposed to correct the recombination fraction between epistatic distorted markers in backcross and F2 populations under the framework of fitness and liability models. The information for three or four markers flanking with an epistatic segregation distortion locus was used to estimate the recombination fraction by the maximum likelihood method, implemented via an expectation-maximisation algorithm. A set of Monte Carlo simulation experiments along with a real data analysis in rice was performed to validate the new method. The results showed that the estimates from the new method are unbiased. In addition, five statistical properties for the new method in a backcross were summarised and confirmed by theoretical, simulated and real data analyses.

Multi-QTL mapping for quantitative traits using epistatic distorted markers.

The interaction between segregation distortion loci (SDL) has been often observed in all kinds of mapping populations. However, little has been known about the effect of epistatic SDL on quantitative trait locus (QTL) mapping. Here we proposed a multi-QTL mapping approach using epistatic distorted markers. Using the corrected linkage groups, epistatic SDL was identified. Then, these SDL parameters were used to correct the conditional probabilities of QTL genotypes, and these corrections were further incorporated into the new QTL mapping approach. Finally, a set of simulated datasets and a real data in 304 mouse F2 individuals were used to validate the new method. As compared with the old method, the new one corrects genetic distance between distorted markers, and considers epistasis between two linked SDL. As a result, the power in the detection of QTL is higher for the new method than for the old one, and significant differences for estimates of QTL parameters between the two methods were observed, except for QTL position. Among two QTL for mouse weight, one significant difference for QTL additive effect between the above two methods was observed, because epistatic SDL between markers C66 and T93 exists (P = 2.94e-4).

An S-Locus Independent Pollen Factor Confers Self-Compatibility in ‘Katy’ Apricot

Loss of pollen-S function in Prunus self-compatible cultivars has been mostly associated with deletions or insertions in the S-haplotype-specific F-box (SFB) genes. However, self-compatible pollen-part mutants defective for non-S-locus factors have also been found, for instance, in the apricot (Prunus armeniaca) cv. ‘Canino’. In the present study, we report the genetic and molecular analysis of another self-compatible apricot cv. termed ‘Katy’. S-genotype of ‘Katy’ was determined as S 1 S 2 and S-RNase PCR-typing of selfing and outcrossing populations from ‘Katy’ showed that pollen gametes bearing either the S 1- or the S 2-haplotype were able to overcome self-incompatibility (SI) barriers. Sequence analyses showed no SNP or indel affecting the SFB 1 and SFB 2 alleles from ‘Katy’ and, moreover, no evidence of pollen-S duplication was found. As a whole, the obtained results are compatible with the hypothesis that the loss-of-function of a S-locus unlinked factor gametophytically expressed in pollen (M’-locus) leads to SI breakdown in ‘Katy’. A mapping strategy based on segregation distortion loci mapped the M’-locus within an interval of 9.4 cM at the distal end of chr.3 corresponding to ∼1.29 Mb in the peach (Prunus persica) genome. Interestingly, pollen-part mutations (PPMs) causing self-compatibility (SC) in the apricot cvs. ‘Canino’ and ‘Katy’ are located within an overlapping region of ∼273 Kb in chr.3. No evidence is yet available to discern if they affect the same gene or not, but molecular markers seem to indicate that both cultivars are genetically unrelated suggesting that every PPM may have arisen independently. Further research will be necessary to reveal the precise nature of ‘Katy’ PPM, but fine-mapping already enables SC marker-assisted selection and paves the way for future positional cloning of the underlying gene.

The maternal cytoplasmic environment may be involved in the viability selection of gametes and zygotes.

Segregation distortion is the phenomenon whereby the observed genotypic frequencies of a locus fall outside the expected Mendelian segregation ratio, and it is increasingly recognised as a potentially powerful evolutionary force. The main reason for segregation distortion is a difference in the viability of gametes and zygotes caused by viability loci in the segregating progeny. However, the maternal cytoplasm may also be involved in the viability selection of gametes and zygotes. The objectives of this study were to map the segregation distortion loci (SDL) in maize and to test the hypothesis that the viability of gametes and zygotes may also be associated with the maternal cytoplasmic environment. In the present study, a reciprocal mating design was conducted to generate an F2-segregating population. A linkage map was constructed with 126 microsatellite markers. A whole-genome scan was performed to detect the SDL in segregating populations with different maternal cytoplasm environments. Altogether, 14 SDL with strong LOD (logarithm (base 10) of odds) supports were identified in the specifically designed F2 populations. Interestingly, we found dramatic changes in the genotypic frequencies of the SDL in the two maternal cytoplasmic backgrounds, which indicated a change in the viability of gametes and zygotes in different cytoplasmic environments. Furthermore, in the JB cytoplasmic background, most of the detected SDL and complete distortion markers exhibited similar bias patterns favouring the Y53 alleles. These results suggested that selfish cytoplasmic elements may have an important role in shaping the patterns of segregation distortion in F2 populations through selective viability of gametes and zygotes.

Multi-QTL mapping for quantitative traits using distorted markers

Marker segregation distortion is a common natural phenomenon. However, relatively little is known about utilizing distorted markers for detecting quantitative trait loci (QTL). Therefore, in this study we proposed a multi-QTL mapping approach that uses distorted markers. First, the information from all markers, including distorted markers, was used to detect segregation distortion loci (SDL). Second, the information from the detected SDL was used to correct the conditional probabilities of the QTL genotypes conditional on marker information, and these corrected probabilities were then incorporated into a multi-QTL mapping methodology. Finally, the proposed approach was validated by both Monte Carlo simulation studies and real data analysis. The results from the simulation studies show that as long as one or two SDL are placed around the simulated QTL, there are no differences between the new method and the ordinary interval mapping method in terms of the power of QTL detection or the estimates of the position and dominant effects of the QTL. However, the power of QTL detection is higher under the dominant genetic model of SDL than under the additive genetic model, and the estimate for the additive effect of QTL using the new method is significantly different from the estimate obtained using ordinary interval mapping. The above results were further confirmed by the detection of QTL for dried soymilk in 222 F2:4 families in soybean.

Physical mapping of a pollen modifier locus controlling self-incompatibility in apricot and synteny analysis within the Rosaceae

S-locus products (S-RNase and F-box proteins) are essential for the gametophytic self-incompatibility (GSI) specific recognition in Prunus. However, accumulated genetic evidence suggests that other S-locus unlinked factors are also required for GSI. For instance, GSI breakdown was associated with a pollen-part mutation unlinked to the S-locus in the apricot (Prunus armeniaca L.) cv. 'Canino'. Fine-mapping of this mutated modifier gene (M-locus) and the synteny analysis of the M-locus within the Rosaceae are here reported. A segregation distortion loci mapping strategy, based on a selectively genotyped population, was used to map the M-locus. In addition, a bacterial artificial chromosome (BAC) contig was constructed for this region using overlapping oligonucleotides probes, and BAC-end sequences (BES) were blasted against Rosaceae genomes to perform micro-synteny analysis. The M-locus was mapped to the distal part of chr.3 flanked by two SSR markers within an interval of 1.8cM corresponding to ~364Kb in the peach (Prunus persica L. Batsch) genome. In the integrated genetic-physical map of this region, BES were mapped against the peach scaffold_3 and BACs were anchored to the apricot map. Micro-syntenic blocks were detected in apple (Malus×domestica Borkh.) LG17/9 and strawberry (Fragaria vesca L.) FG6 chromosomes. The M-locus fine-scale mapping provides a solid basis for self-compatibility marker-assisted selection and for positional cloning of the underlying gene, a necessary goal to elucidate the pollen rejection mechanism in Prunus. In a wider context, the syntenic regions identified in peach, apple and strawberry might be useful to interpret GSI evolution in Rosaceae.

Detection of segregation distortion loci in triticale (x Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map

BackgroundTriticale is adapted to a wide range of abiotic stress conditions, is an important high-quality feed stock and produces similar grain yield but more biomass compared to other crops. Modern genomic approaches aimed at enhancing breeding progress in cereals require high-quality genetic linkage maps. Consensus maps are genetic maps that are created by a joint analysis of the data from several segregating populations and different approaches are available for their construction. The phenomenon that alleles at a locus deviate from the Mendelian expectation has been defined as segregation distortion. The study of segregation distortion is of particular interest in doubled haploid (DH) populations due to the selection pressure exerted on the plants during the process of their establishment.ResultsThe final consensus map, constructed out of six segregating populations derived from nine parental lines, incorporated 2555 DArT markers mapped to 2602 loci (1929 unique). The map spanned 2309.9 cM with an average number of 123.9 loci per chromosome and an average marker density of one unique locus every 1.2 cM. The R genome showed the highest marker coverage followed by the B genome and the A genome. In general, locus order was well maintained between the consensus linkage map and the component maps. However, we observed several groups of loci for which the colinearity was slightly uneven. Among the 2602 loci mapped on the consensus map, 886 showed distorted segregation in at least one of the individual mapping populations. In several DH populations derived by androgenesis, we found chromosomes (2B, 3B, 1R, 2R, 4R and 7R) containing regions where markers exhibited a distorted segregation pattern. In addition, we observed evidence for segregation distortion between pairs of loci caused either by a predominance of parental or recombinant genotypes.ConclusionsWe have constructed a reliable, high-density DArT marker consensus genetic linkage map as a basis for genomic approaches in triticale research and breeding, for example for multiple-line cross QTL mapping experiments. The results of our study exemplify the tremendous impact of different DH production techniques on allele frequencies and segregation distortion covering whole chromosomes.

Erratum to: A segregation distortion locus located on linkage group 4 of the chickpea genetic map

Erratum to: A segregation distortion locus located on linkage group 4 of the chickpea genetic map

Identification of QTLs for hybrid fertility in inter-subspecific crosses of rice (Oryza sativa L.)

Two subspecies in rice, japonica and indica, have their own ecotypic traits. However, reproductive barriers such as spikelet sterility in hybrid progenies between subspecies have been an obstacle in breeding programs for combining desirable traits from both subspecies through inter-subspecific hybridization. The 166 F9 RILs and two BC1F1s’ were analyzed for spikelet and pollen fertility with the parents and F1 between Dasanbyeo (DS, indica) / TR22183 (TR, japonica). A frame map was constructed using a total of 218 polymorphic STS and SSR markers. In both BC1F1s’ of DS//DS/TR and TR//DS/TR, clusters of significant QTLs for spikelet and pollen fertility were identified on the short arm of chromosome 5 and chromosome 8. Nine and ten digenic epistatic interactions for DS//DS/TR and TR//DS//TR were identified, respectively. HF-QTLs were detected at the similar position with subspecies-specific markers and segregation distortion loci, implying that HF-QTLs might be associated with the differentiation of indica and japonica. Hybrid fertility/sterility and its relationship with other traits are discussed in relation to the reproductive barriers between subspecies of rice.