Reciprocal Backcross Research Articles

Inheritance of Resistance to Bacterial Halo Blight and Bacterial Leaf Spot in Arabica Coffee.

Developing coffee cultivars resistant to multiple diseases by combining resistance genes is a top priority in breeding programs. To create cultivars resistant to diseases and nematodes, we transferred genes for resistance to bacterial infections caused by Pseudomonas coronafaciens pv. garcae, which causes bacterial halo blight (BHB), and P. amygdali pv. tabaci, which causes bacterial leaf spots (BLS), into Arabica coffee. Genetic analyses were conducted on breeding populations to estimate the number and function of genes that confer resistance to BHB and BLS. In total, 2,109 plants in the F2 generation and reciprocal backcrosses were inoculated with P. coronafaciens pv. garcae, while 1,996 plants were inoculated with P. amygdali pv. tabaci. Results showed that resistance to both pathogens had a heritability of 0.99, and the segregations of resistance indicated that each disease was controlled by a single dominant gene. The analyses also revealed that the resistance genes for BHB and BLS were linked, with an average distance of 10.75 cM between them on the same chromosome.

Backcrossing as a species restoration technique.

An investigation was conducted on the phenotypic results of mouse hybridization and seven generations of backcrossing, observing reciprocal F1 hybrids and backcrosses of Mus spretus and a laboratory strain of Mus domesticus C57BL/6J. F1 hybrids, backcrosses, and pure control specimens were measured for 6 body characteristics, 4 pelage coloration characteristics, 14 behaviors, and reproduction as reflected in litter size. Backcrossing was pursued for seven generations to FBC7 (i.e., "Backcross 7" or seven generations from commencement of backcrossing from an F1 hybrid female) where species restoration is mathematically calculated to be at 99.7%. Except for a minority of FBC7 M. spretus specimens failing to conform completely to one pelage characteristic, FBC7 specimens were indistinguishable from controls both subjectively and in all areas of measurement. The M. spretus backcross line was followed generation by generation and was largely conforming to controls by FBC4 at latest. The same effect was observed in the reciprocal M. domesticus backcross line. Fertility was negatively affected in F1 hybrids but restored or improved in backcross generations. Discussion is offered on hybridization and backcrossing as it occurs in nature and how it has been used or could be used as an additional ex situ tool in wildlife conservation efforts. It is concluded that conservation-oriented backcrossing is a practical species/subspecies restoration technique and has the potential to make genetic rescue feasible with minimal gene flow at the binomial level. Backcrossing is most applicable in closely monitored ex situ settings (1) where only one sex remains of a given taxon; and (2) where inbreeding depression seriously threatens a remnant taxon's ability to recover, and the only gene flow option is from another distinct species.

Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genus Sebastes).

Postmating isolation is thought to be an important driver of the late stages of speciation. However, relatively little is empirically known about the process compared with other isolating mechanisms that drive the early stages of speciation, especially in non-model organisms. We characterized the genetic architecture of postmating isolation between 2 rockfishes, Sebastes schlegelii and S. trivittatus, whose reproductive isolation is complete. We examined transmission ratio distortion (TRD) patterns of genetic markers in 2 reciprocal backcross populations. Markers showing either of the 2 types of TRD was widespread across the genome, with some of the distorted markers forming extensive clusters around the recombination coldspots. These suggest that the postmating isolation effectively prevents gene flow across the genome and the recombination landscape contributes to the genetic architecture. Comparisons between 2 backcross families and 2 developmental stages showed little similarity in the distorted markers, suggesting asymmetry and stage specificity of the isolation. This may be due to hybrid incompatibility involving maternal factors or extrinsic selection. The lack of sex-ratio distortion in the mapping families suggested that Haldane's rule in terms of hybrid inviability does not hold. Additionally, quantitative trait loci (QTL) mapping detected significant QTLs for sex and the morphological traits relevant to speciation and convergence of rockfishes, including body coloration. Genes in the melanocortin system, including agouti-signaling protein 1 (asip1) and melanocortin 1 receptor (mc1r), might underlie the horizontal and vertical color patterns on the body, respectively. These findings constitute an essential step toward a comprehensive understanding of speciation and morphological diversification of rockfishes.

Both male and female meiosis contribute to non-Mendelian inheritance of parental chromosomes in interspecific plant hybrids (Lolium × Festuca).

Some interspecific plant hybrids show unequal transmission of chromosomes from parental genomes to the successive generations. It has been suggested that this is due to a differential behavior of parental chromosomes during meiosis. However, underlying mechanism is unknown. We analyzed chromosome composition of the F2 generation of Festuca × Lolium hybrids and reciprocal backcrosses to elucidate effects of male and female meiosis on the shift in parental genome composition. We studied male meiosis, including the attachment of chromosomes to the karyokinetic spindle and gene expression profiling of the kinetochore genes. We found that Lolium and Festuca homoeologues were transmitted differently to the F2 generation. Female meiosis led to the replacement of Festuca chromosomes by their Lolium counterparts. In male meiosis, Festuca univalents were attached less frequently to microtubules than Lolium univalents, lagged in divisions and formed micronuclei, which were subsequently eliminated. Genome sequence analysis revealed a number of non-synonymous mutations between copies of the kinetochore genes from Festuca and Lolium genomes. Furthermore, we found that outer kinetochore proteins NDC80 and NNF1 were exclusively expressed from the Lolium allele. We hypothesize that silencing of Festuca alleles results in improper attachment of Festuca chromosomes to karyokinetic spindle and subsequently their gradual elimination.

Comparative transmission genetics of introgressed chromatin in reciprocal advanced backcross populations in Gossypium (cotton) polyploids.

Introgression is a potential source of valuable genetic variation and interspecific introgression lines are important resources for plant breeders to access novel alleles. Experimental advanced-generation backcross populations contain individuals with genomic compositions similar to those resulting from natural interspecific hybridization and provide opportunities to study the nature and transmission pattern of donor chromatin in recipient genomes. Here, we analyze transmission of donor chromatin in reciprocal backcrosses between G. hirsutum and G. barbadense. Across the genome, recurrent backcrossing in both backgrounds yielded donor chromatin at slightly higher frequencies than the Mendelian expectation in BC5F1 plants, while the average frequency of donor alleles in BC5F2 segregating families was less than expected. In the two subgenomes of polyploid cotton, the rate of donor chromatin introgression was similar. Although donor chromatin was tolerated over much of the recipient genomes, 21 regions recalcitrant to donor alleles were identified. Only limited correspondence is observed between the recalcitrant regions in the two backgrounds, suggesting the effect of species background on introgression of donor segments. Genetic breakdown was progressive, with floral abscission and seed inviability ongoing during backcrossing cycles. Regions of either high or low introgression tended to be in terminal chromosomal regions that are generally rich in both genes and crossover events, with long stretches around the centromere having limited crossover activity resulting in relatively constant low introgression frequencies. Constraints on fixation and selection of donor alleles highlights the challenges of utilizing introgression breeding in crop improvement.

Wild and cultivated allele effects on rice phenotypic traits in reciprocal backcross populations between Oryza rufipogon and two cultivars, O. sativa Nipponbare and IR36.

A total of four populations of reciprocal backcross recombinant inbred lines were produced from a cross between a wild accession of Oryza rufipogon W630 and two major cultivars, O. sativa Japonica Nipponbare and Indica IR36. Using these populations, quantitative trait locus (QTL) analysis for eight morphological traits (culm length, panicle length, days to heading, panicle shape, pericarp color, hull color, seed shattering and seed awning) was carried out, and the putative QTL regions were compared among the populations. The QTLs with strong allele effects were commonly detected for culm length, panicle shape, pericarp color and hull color in all four populations, and their peak locations were close to the major genes of sd1, Spr3, Rc and Bh4, respectively. For panicle length and days to heading, some QTL regions overlapped between two or three populations. In the case of seed shattering and seed awning, strong wild allele effects at major loci were observed only in the populations with cultivated backgrounds. Since the wild and cultivated alleles have never been evaluated in the reciprocal genetic backgrounds, the present results provide new information on gene effects in breeding and domestication studies.

Experimental introgression in Drosophila: Asymmetric postzygotic isolation associated with chromosomal inversions and an incompatibility locus on the X chromosome.

Interspecific gene flow (introgression) is an important source of new genetic variation, but selection against it can reinforce reproductive barriers between interbreeding species. We used an experimental approach to trace the role of chromosomal inversions and incompatibility genes in preventing introgression between two partly sympatric Drosophila virilis group species, D.flavomontana and D.montana. We backcrossed F1 hybrid females from a cross between D.flavomontana female and D.montana male with the males of the parental species for two generations and sequenced pools of parental strains and their reciprocal second generation backcross (BC2 mon and BC2 fla) females. Contrasting the observed amount of introgression (mean hybrid index, HI) in BC2 female pools along the genome to simulations under different scenarios allowed us to identify chromosomal regions of restricted and increased introgression. We found no deviation from the HI expected under a neutral null model for any chromosome for the BC2 mon pool, suggesting no evidence for genetic incompatibilities in backcrosses towards D.montana. In contrast, the BC2 fla pool showed high variation in the observed HI between different chromosomes, and massive reduction of introgression on the X chromosome (large X-effect). This observation is compatible with reduced recombination combined with at least one dominant incompatibility locus residing within the X inversion(s). Overall, our study suggests that genetic incompatibilities arising within chromosomal inversions can play an important role in speciation.

Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode.

Different modes of reproduction evolve rapidly, with important consequences for genome composition. Selfing species often occupy a similar niche as their outcrossing sister species with which they are able to mate and produce viable hybrid progeny, raising the question of how they maintain genomic identity. Here, we investigate this issue by using the nematode Caenorhabditis briggsae, which reproduces as a hermaphrodite, and its outcrossing sister species Caenorhabditis nigoni We hypothesize that selfing species might develop some barriers to prevent gene intrusions through gene regulation. We therefore examined gene regulation in the hybrid F2 embryos resulting from reciprocal backcrosses between F1 hybrid progeny and C. nigoni or C. briggsae F2 hybrid embryos with ∼75% of their genome derived from C. briggsae (termed as bB2) were inviable, whereas those with ∼75% of their genome derived from C. nigoni (termed as nB2) were viable. Misregulation of transposable elements, coding genes, and small regulatory RNAs was more widespread in the bB2 compared with the nB2 hybrids, which is a plausible explanation for the differential phenotypes between the two hybrids. Our results show that regulation of the C. briggsae genome is strongly affected by genetic exchanges with its outcrossing sister species, C. nigoni, whereas regulation of the C. nigoni genome is more robust on genetic exchange with C. briggsae The results provide new insights into how selfing species might maintain their identity despite genetic exchanges with closely related outcrossing species.

Concurrent improvement of durum and emmer wheat through reciprocal backcrossing and hybridization

AbstractEmmer wheat has not been improved but is a valuable gene source for improving durum (Triticum turgidum ssp. durum). Conversely, durum is less looked upon for emmer (T. turgidum ssp. dicoccum) improvement. This study examined the possibility of concurrently improving the two species by crossing eight durum cultivars with four emmer local varieties in a half‐diallel fashion in two consecutive years. Also, emmer and two durum genotypes were reciprocally backcrossed, and their BC1F1 progeny were field‐evaluated during the wheat cropping season (November–June) at the Isfahan University of Technology research farm (32°32′ N, 51°23′ E). The results showed that durum wheat had a considerable effect on the grain yield (GY), kernel diameter, 1,000‐kernel weight (TKW), and test weight of F1 hybrids, whereas emmer contributed more to increasing the grain protein content (GPC), kernel length, and plant height (PH). A similar pattern was observed for BC1F1 hybrids from the two recurrent durum parents. The GPC was reduced with recurrent durum parents in the backcrosses compared with emmer, but was still higher than in both durum parents. In the backcrosses with the recurrent emmer parent, GY and TKW were higher than those of emmer but only slightly lower than those of the durum parents. The PH was strongly influenced by emmer in all crosses, though the lodging was significantly reduced compared with emmer, possibly through obtaining stronger stems from durum. These findings suggest the possibility of combining desirable genes from the two species and their concurrent improvement in a single breeding program.

Genome-wide recombination variation in biparental segregating and reciprocal backcross populations provides information for introgression breeding in Brassica napus

Variation in patterns of recombination in plant genomes provides information about species evolution, genetic diversity and crop improvement. We investigated meiotic crossovers generated in biparental segregating and reciprocal backcross populations of the allopolyploid genome of rapeseed (Brassica napus) (AACC, 2n = 38). A structured set of 1445 intercrossed lines was derived from two homozygous de novo genome-assembled parents that represented the major genetic clusters of semi-winter Chinese and winter European rapeseeds, and was used to increase QTL resolution and achieve genomic reciprocal introgression. A high-density genetic map constructed with 6161 genetic bins and anchored centromere regions was used to establish the pattern of recombination variation in each chromosome. Around 93% of the genome contained crossovers at a mean rate of 3.8 cM Mb−1, with the remaining 7% attributed to centromeres or low marker density. Recombination hotspots predominated in the A genome, including two-thirds of those associated with breeding introgression from B. rapa. Genetic background might affect recombination variation. Introgression of genetic diversity from European winter to Chinese semi-winter rapeseed showed an increase in crossover rate under the semi-winter environment. Evidence for an elevated recombination rate having historically contributed to selective trait improvement includes accumulation of favorable alleles for seed oil content on hotspots of chromosome A10. Conversely, strong artificial selection may affect recombination rate variation, as appears to be the case with a coldspot resulting from strong selection for glucosinolate alleles on A09. But the cold region would be promptly reactivated by crossing design indicated by the pedigree analysis. Knowledge of recombination hotspots and coldspots associated with QTL for 22 traits can guide selection strategies for introgression breeding between the two gene pools. These results and rich genomic resources broaden our understanding of recombination behavior in allopolyploids and may advance rapeseed genetic improvement.

Identification of small effect quantitative trait loci of plant architectural, flowering, and early maturity traits in reciprocal interspecific introgression population in cotton.

Plant architecture, flowering time and maturity traits are important determinants of yield and fiber quality of cotton. Genetic dissection of loci determining these yield and quality components is complicated by numerous loci with alleles conferring small differences. Therefore, mapping populations segregating for smaller numbers and sizes of introgressed segments is expected to facilitate dissection of these complex quantitative traits. At an advanced stage in the development of reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum cultivar 'Acala Maxxa' (GH) and G. barbadense 'Pima S6' (GB), we undertook mapping of plant architectural traits, flowering time and maturity. A total of 284 BC4F1 and BC4F2 progeny rows, 120 in GH and 164 in GB background, were evaluated for phenotype, with only 4 and 3 (of 7) traits showing significant differences among progenies. Genotyping by sequencing yielded 3,186 and 3,026 SNPs, respectively, that revealed a total of 27 QTLs in GH background and 22 in GB, for plant height, days to flowering, residual flowering at maturity and maturity. More than of 90% QTLs identified in both backgrounds had small effects (%PV < 10), supporting the merit of this population structure to reduce background noise and small effect QTLs. Germplasm developed in this study may serve as potential pre-breeding material to develop improved cotton cultivars.

Diversity of morphological traits and glucosinolate composition in backcross progenies of Brassica rapa L. × Eruca vesicaria (L.) Cav. hybrids

Breeding at both interspecific and intergeneric levels is an effective method for expanding genetic variation of cruciferous crops; however, few commercially accepted varieties have been released because of difficulties in generating fertile progenies. We employed backcross strategy to introduce Eruca vesicaria-specific characteristics into Brassica rapa and successfully obtained four BC1F1 lines that showed a wide range of diversity of morphological traits and glucosinolate (GSL) composition. Thus, leaf shape, anthocyanin coloration, glucoraphanin content, and red petal veins were found to be inherited mainly from E. vesicaria, though most of the morphological characteristics and GSL composition were inherited from intergeneric F1 plants. Since all BC1F1 lines showed post-fertilization barriers, backcrossing with B. rapa was performed and BC2F1 progenies were successfully obtained, which showed diverse morphological characteristics and GSL composition as well as higher regeneration potential. These results suggest that widening of genetic diversity of B. rapa can be achieved through successive reciprocal backcrossing of B. rapa × E. vesicaria hybrids with B. rapa.

Inheritance of Compact Growth Habit, and Investigation of Linkage to Weeping Architecture and Purple Leaf Color in Eastern Redbud (Cercis canadensis L.)

Eastern redbud (Cercis canadensis L.) is a commonly used small landscape tree. Compact growth, purple leaf color, and weeping architecture are three popular ornamental phenotypes. Inheritances of weeping architecture and purple leaves have been reported previously. Inheritance of compact growth habit and its genetic linkage with the weeping and purple leaf genes have not been reported. In the present research, the inheritance of compact growth derived from ‘Ace of Hearts’ was explored in the F1, F2, and reciprocal backcross families resulting from the controlled hybridization of ‘Ruby Falls’ (normal growth/weeping architecture/purple leaf) × ‘Ace of Hearts’ (compact growth/nonweeping architecture/green leaf). All 27 F1 individuals were nonweeping, green-leaved, and noncompact. A total of 572 F2 progeny were obtained, and subsequent analysis of segregation revealed a single recessive gene controlled compact growth habit. Analysis of reciprocal backcross families confirmed this result as well. Weeping architecture and purple leaf color were also controlled by single recessive genes, confirming findings presented in previous studies in another redbud family. No linkage between the three genes was detected. This research is the first to report the inheritance of compact growth in eastern redbud and confirms independent assortment between the compact, purple leaf, and weeping genes.

Effect of feathering genes on growth performance of F2 backcrosses and comparison of F1 and F2 crosses of Abor Acre broiler breeder x native chickens in humid tropical environment

This study was conducted to evaluate growth performance, brooding and rearing mortalities of F2 main and reciprocal backcross progenies of Abor Acre broiler breeder x native chicken crosses and to compare their F1 and F2 backcross progenies. The base population used in the study consisted of mature (~ 48 weeks) male and female native chickens and exotic (Abor Acre) broiler breeder parent stock. The native chicken varieties were made up of normal feather, naked neck and frizzle genotypes. These birds were mated to the Abor Acre broiler parent stocks in main and reciprocal fashion generating F1 main and reciprocal crossbreds. Females of these F1 hybrids were then mated back to the broiler breeder cock to generate F2 main and reciprocal backcross progenies that were evaluated in the present study. Data analyzed include body weight (BWT) and linear body parameters (LBPs), average feed intake (AFI), feed conversion ratio (FCR), brooding and rearing mortalities. Comparisons between genetic groups for these parameters were done by means of analysis of variance (ANOVA) technique. Results indicated improved growth performance and feed conversion ratios in the F2 reciprocal backcross groups compared to their F2 main backcross counterparts. The F2 individuals in both crosses were superior to F1 crossbred populations. Chick mortality rates were higher in main and reciprocal backcross groups involving the naked neck genotype compared to other plumage types. It was concluded that backcrossing the F1 individuals to the exotic broiler breeder cocks increased the genetic profile of the backcross lines resulting in enhanced growth performance of progenies. Crossbreeding of exotic and local chicken varieties generated progenies that had higher genetic potentials for growth relative to the local strains and better adaptability relative to the exotic breed. However, incubation and brooding strategies capable of minimizing mortalities at embryonic, brooding and rearing phases should be explored and integrated in local chicken improvement programmes involving the use of these plumage reducing genes for optimal results.

Relative fitness and stability of resistance in a near-isogenic strain of indoxacarb resistant Helicoverpa armigera (Lepidoptera: Noctuidae).

A strain of Helicoverpa armigera with 171-fold resistance to indoxacarb was introgressed with a susceptible strain by serial backcrossing and reselection with indoxacarb resulting in the creation of the near-isogenic GY7-39BC4 strain. Fitness was compared on artificial diet under diapause and non-diapause conditions in resistant, susceptible and F1 progeny from a reciprocal backcross of the two strains using life history trait analyses. Selection experiments were used to determine stability of resistance. There were no significant differences between strains in survival, female fertility or realized fecundity. A comparison of the intrinsic rate of population increase showed similar relative fitness between strains. Lower male fertility and male longevity in the resistant strain and one of the F1 strains compared with the susceptible strain suggests small non-recessive costs may be associated with male reproductive capacity in individuals with indoxacarb resistance alleles. However, there was no significant decline in resistance in the GY7-39 strain when reared in the absence of insecticide for five generations. Following an artificially induced diapause, survival was reduced by 52% and pupal weights were significantly lower in the resistant strain compared with the susceptible strain. These results suggest indoxacarb resistance does not confer a major fitness cost under standard laboratory conditions. However, a survival cost associated with overwintering highlights the imperative for adoption of management strategies in northern regions of Australia where a winter diapause does not occur. © 2020 Society of Chemical Industry.

Realized heritability, inheritance and cross-resistance patterns in imidacloprid-resistant strain of Dysdercus koenigii (Fabricius) (Hemiptera: Pyrrhocoridae).

Imidacloprid, a neonicotinoid insecticide, is widely sprayed alone or mixed with other insecticides against Dysdercus koenigii, a potential pest of cotton in Pakistan. Recently, resistance to imidacloprid in field populations of D. koenigii has developed because of its overuse. Herein, we have investigated inheritance of imidacloprid resistance in D. koenigii and its cross-resistance to other insecticides. The imidacloprid-selected population had a 91 421-fold increase in resistance to imidacloprid after six generations. Overlapping 95% fiducial limits of LC50s of the F1 (Imida-Sel ♂ × Sus-ST ♀) and F1 † (Imida-Sel ♀ × Sus-ST ♂) suggested an autosomal and incomplete dominant resistance to imidacloprid (DLC = 0.84 for F1 and 0.86 for F1 † ). Reciprocal backcrosses of the F1 and F1 † with Sus-ST predicted a polygenic inheritance. Realized heritability of imidacloprid resistance was 0.38. When mean slope = 1.74 and h2 = 0.38, then 3-13 generations would be required for a ten-fold increase in LC50s at 90-20% intensity of selection. Very high cross-resistance to emamectin benzoate (143-fold), deltamethrin (1675-fold) and lambda-cyhalothrin (140-fold), and moderate cross-resistance to acetamiprid (37-fold) in the imidacloprid-selected strain compared to the field population were observed. Imidacloprid resistance developed very quickly under continuous selection pressure in the laboratory. These factors might lead to an increasing likelihood of resistance development in field populations, if imidacloprid is used continuously without insecticide rotation for prolonged periods. The present results would be supportive for better management of D. koenigii by devising an effective resistance management strategy. © 2020 Society of Chemical Industry.

Identification and QTL mapping of resistance to Turnip yellows virus (TuYV) in oilseed rape, Brassica napus

Key messagePartially dominant resistance to Turnip yellows virus associated with one major QTL was identified in the natural allotetraploid oilseed rape cultivar Yudal.Turnip yellows virus (TuYV) is transmitted by the peach-potato aphid (Myzus persicae) and causes severe yield losses in commercial oilseed rape crops (Brassica napus). There is currently only one genetic resource for resistance to TuYV available in brassica, which was identified in the re-synthesised B. napus line ‘R54’. In our study, 27 mostly homozygous B. napus accessions, either doubled-haploid (DH) or inbred lines, representing a diverse subset of the B. napus genepool, were screened for TuYV resistance/susceptibility. Partial resistance to TuYV was identified in the Korean spring oilseed rape, B. napus variety Yudal, whilst the dwarf French winter oilseed rape line Darmor-bzh was susceptible. QTL mapping using the established Darmor-bzh × Yudal DH mapping population (DYDH) revealed one major QTL explaining 36% and 18% of the phenotypic variation in two independent experiments. A DYDH line was crossed to Yudal, and reciprocal backcross (BC1) populations from the F1 with either the susceptible or resistant parent revealed the dominant inheritance of the TuYV resistance. The QTL on ChrA04 was verified in the segregating BC1 population. A second minor QTL on ChrC05 was identified in one of the two DYDH experiments, and it was not observed in the BC1 population. The TuYV resistance QTL in ‘R54’ is within the QTL interval on Chr A04 of Yudal; however, the markers co-segregating with the ‘R54’ resistance are not conserved in Yudal, suggesting an independent origin of the TuYV resistances. This is the first report of the QTL mapping of TuYV resistance in natural B. napus.

Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis.

SummaryDuring meiosis, recombination ensures allelic exchanges through crossovers (COs) between the homologous chromosomes. Advances in our understanding of the rules of COs have come from studies of mutations including structural chromosomal rearrangements that, when heterozygous, are known to impair COs in various organisms. In this work, we investigate the effect of a large heterozygous pericentric inversion on male and female recombination in Arabidopsis. The inversion was discovered in the Atmcc1 mutant background and was characterized through genetic and next‐generation sequencing analysis. Reciprocal backcross populations, each consisting of over 400 individuals, obtained from the mutant and the wild type, both crossed with Landsberg erecta, were analyzed genome‐wide by 143 single‐nucleotide polymorphisms. The negative impact of inversion became evident in terms of CO loss in the rearranged chromosome in both male and female meiosis. No single‐CO event was detected within the inversion, consistent with a post‐meiotic selection operating against unbalanced gametes. Cytological analysis of chiasmata in F1 plants confirmed that COs were reduced in male meiosis in the chromosome with inversion. Crossover suppression on the rearranged chromosome is associated with a significant increase of COs in the other chromosomes, thereby maintaining unchanged the number of COs per cell. The CO pattern observed in our study is consistent with the interchromosomal (IC) effect as first described in Drosophila. In contrast to male meiosis, in female meiosis no IC effect is visible. This may be related to the greater strength of interference that constrains the CO number in excess of the minimum value imposed by CO assurance in Arabidopsis female meiosis.

Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

BackgroundHigh-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species.ResultsIn the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73 cM and 0.55 cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8–15.7% of the total growth-traits variation.ConclusionsThe genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growth traits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps.

Dissecting the quantitative variations of threshability in rice (&lt;i&gt;Oryza sativa&lt;/i&gt; L.)

In rice, low threshability retains grains on the panicles especially in japonica rice ( O. sativa subsp. Japonica ) and high threshability makes it easier for harvesting in indica. The genetic mechanisms underlying moderate threshability in rice remain largely unclear. A set of reciprocal Backcross Inbred Lines BILs including 226 and 229 lines from indica rice ( O. sativa subsp. indica) and japonica rice (O. sativa subsp. japonica) backgrounds, respectively, and 262 recombinant inbred lines RILs developed from same cross between an indica, were adopted for testing threshability in two seasons. Percentages of dislodged grains were estimated at the maturity, harvesting and after sun drying. A total of 265 SNP markers developed based on sequencing and evenly distributed throughout the 12 chromosomes were used for genotyping assay. Inclusive composite interval mapping (ICIM) was used to dissect genomic regions and interactions affecting quantitative variation of threshability. A total of 13 QTLs were found to be conferring quantitative variations of threshability, which were distributed on all chromosomes. Two known major genes (QTLs) qSH1 and sh4 were also present. New additive QTLs, qThr1-a, qThr2, qThr3 qThr7, qThr8, qThr10, qThr11 and qThr12 were found as well. Twenty-four epistatics QTLs of which eight were common in both japonica and indica backgrounds were detected in two consecutive seasons. The overall threshability explained by all additive and interacting QTLs (R2) were 70% and 1 for indica, 15 and 8% for japonica and 17.4 and 10.6% for RIL backgrounds, respectively. Findings have preliminarily revealed a relatively complex mechanism underlying the quantitative variations of threshability in rice, which was controlled not only by major loci but also affected by epistasis and genetic background effects. Key words : epistasis, genetic background effect, quantitative variation, rice ( Oryza sativa L .), threshability