The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping

Recombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence‐based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome‐wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans‐acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans‐acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low‐recombining pericentromeric regions of chromosomes.     

A high‐density linkage map enables a second‐generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to develop a high‐density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best‐order map contained 4215 markers, with a total distance of 3132 cM and a mean genetic distance between markers of 0.12 cM . Facilitated by the array being designed to include markers from most scaffolds, we obtained a second‐generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super‐scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cM /Mb and correlated closely with chromosome size, from 2 cM /Mb for chromosomes >100 Mb to >10 cM /Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cM was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes.     

Genomic analysis and marker development for the Tsn1 locus in wheat using bin-mapped ESTs and flanking BAC contigs

The wheat Tsn1 gene confers sensitivity to the host-selective toxin Ptr ToxA produced by the tan spot fungus (Pyrenophora tritici-repentis). The long-term goal of this research is to isolate Tsn1 using a positional cloning approach. Here, we evaluated 54 ESTs (expressed sequence tags) physically mapped to deletion bin 5BL 0.75–0.76, which is a gene-rich region containing Tsn1. Twenty-three EST loci were mapped as either PCR-based single-stranded conformational polymorphism or RFLP markers in a low-resolution wheat population. The genetic map corresponding to the 5BL 0.75–0.76 deletion bin spans 18.5 cM and contains 37 markers for a density of 2 markers/cM. The EST-based genetic map will be useful for tagging other genes, establishing colinearity with rice, and anchoring sequence ready BAC contigs of the 5BL 0.75–0.76 deletion bin. High-resolution mapping showed that EST-derived markers together with previously developed AFLP-derived markers delineated Tsn1 to a 0.8 cM interval. Flanking markers were used to screen the Langdon durum BAC library and contigs of 205 and 228 kb flanking Tsn1 were assembled, sequenced, and anchored to the genetic map. Recombination frequency averaged 760 kb/cM across the 228 kb contig, but no recombination was observed across the 205 kb contig resulting in an expected recombination frequency of more than 10 Mb/cM. Therefore, chromosome walking within the Tsn1 region may be difficult. However, the sequenced BACs allowed the identification of one microsatellite in each contig for which markers were developed and shown to be highly suitable for marker-assisted selection of Tsn1.     

Genetic diversity and linkage disequilibrium studies on a 3.1-Mb genomic region of chromosome 3B in European and Asian bread wheat (Triticum aestivum L.) populations

Genetic diversity and linkage disequilibrium (LD) were investigated in 376 Asian and European accessions of bread wheat (Triticum aestivum L.). After a first and rapid screening about diversity and genetic structure at the whole genome scale using 70 simple sequence repeats (SSRs), we focused on a sequenced contig (ctg954) of 3.1 Mb located on the short arm of chromosome 3B of cv. Chinese Spring, using 32 SSRs and 10 single nucleotide polymorphisms. This contig is part of a multiple fungal resistance region. Mean polymorphism information content value on the 32 SSRs was slightly higher in the Asian genepool (0.396) than that for the European (0.329) pool. Compared with results at the whole genome scale, data from this 3.1-Mb region indicated similar trends in genetic diversity indices between both genepools. Population structure and molecular variance analyses demonstrated significant genetic differentiation and geographical subdivision in both groups of accessions. Concerning LD at the contig level, the European population had a significantly higher mean r ² value (0.23) than the Asian population (0.18), indicating a stronger LD in the European material. With a mean of 1 marker every 74 kb, the resolution reached here allowed to perform a detailed comparative analysis of the LD and genetic diversity along the complete 3.1-Mb region in both genepools. A sliding-window approach revealed some interesting regions of the contig where LD is increasing when genetic diversity is decreasing. This study provides an in-depth understanding of molecular population genetics in European and Asian wheat gene pools, and prospects for association mapping of important sources of fungal disease resistance.     

Localization of<Emphasis Type="Italic"> jointless-2</Emphasis> gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping

Abstract Abscission is a universal process whereby plants shed their organs, such as flowers, fruit and leaves. In tomato, the non-allelic mutations jointless and jointless-2 have been discovered as recessive mutations that completely suppress the formation of pedicel abscission zones. A high resolution genetic map of jointless-2 was constructed using 1,122 jointless F₂ plants. Restriction fragment length polymorphism (RFLP) marker RPD140 completely co-segregated with the jointless-2 locus and mapped in a 2.4 cM interval between RFLP markers CD22 and TG618. To chromosome walk to jointless-2, all three markers were used to screen a bacterial artificial chromosome (BAC) library and contigs were developed. Intensive efforts to expand and merge the BAC contigs were unsuccessful because of the highly repetitive sequence content on the distal ends of each contig. To determine the physical distance between and the orientation of the three contigs, we used high resolution pachytene fluorescence in situ hybridization (FISH) mapping. The RPD140 contig was positioned in the centromeric region of chromosome 12 between two large pericentric heterochromatin blocks, about 50 Mb from the TG618 contig on the short arm and 10 Mb from the CD22 contig on the long arm, respectively. Based on high resolution genetic and physical mapping, we conclude that the jointless-2 gene is located within or near the chromosome 12 centromere where 1 cM is approximately 25 Mb in length.Communicated by Q. ZhangM.A. Budiman, S-B. Chang and S. Lee contributed equally to the work.     

Development of SNP markers linked to the <Emphasis Type="Italic">L</Emphasis> locus in <Emphasis Type="Italic">Capsicum</Emphasis> spp. by a comparative genetic analysis

In pepper, the TMV resistance locus L is syntenic to the tomato I2 and the potato R3 loci on chromosome 11. In this report, we identified pepper bacterial artificial chromosome (BAC) clones corresponding to the I2 and R3 loci and developed L-linked markers using the BAC sequence information. A BAC library was screened using the tomato I2C-1 gene as a probe. The resulting clones were sorted further by PCR screening, sequencing, and genetic mapping. A linkage analysis revealed that BAC clone 082F03 could be anchored to the target region near TG36 on chromosome 11. Using the 082F03 sequence, more BAC clones were identified and a BAC contig spanning 224 kb was constructed. Gene prediction analysis showed that there were at least three I2/R3 R gene analogs (RGAs) in the BAC contig. Three DNA markers closely linked (about 1.2 cM) to the L ⁴ gene were developed by using the BAC contig sequence. The single nucleotide polymorphism marker 087H3T7 developed in this study was subjected to linkage analysis in L ⁴ - and L ³ -segregating populations together with previously developed markers. The 189D23M marker, which is known to co-segregate with L ³ , was located on the opposite side of 087H3T7, about 0.7 cM away from L ⁴ . This supports the idea that L ³ and L ⁴ may be different genes closely linked within the region instead of different alleles at the same locus. Finally, use of flanking markers in molecular breeding program for introgression of L ⁴ to elite germplasm against most aggressive tobamoviruses pathotype P_1,2,3 is discussed.     

Sex-specific crossover distributions and variations in interference level along Arabidopsis thaliana chromosome 4

In many species, sex-related differences in crossover (CO) rates have been described at chromosomal and regional levels. In this study, we determined the CO distribution along the entire Arabidopsis thaliana Chromosome 4 (18 Mb) in male and female meiosis, using high density genetic maps built on large backcross populations (44 markers, >1,300 plants). We observed dramatic differences between male and female map lengths that were calculated as 88 cM and 52 cM, respectively. This difference is remarkably parallel to that between the total synaptonemal complex lengths measured in male and female meiocytes by immunolabeling of ZYP1 (a component of the synaptonemal complex). Moreover, CO landscapes were clearly different: in particular, at both ends of the map, male CO rates were higher (up to 4-fold the mean value), whereas female CO rates were equal or even below the chromosomal average. This unique material gave us the opportunity to perform a detailed analysis of CO interference on Chromosome 4 in male and female meiosis. The number of COs per chromosome and the distances between them clearly departs from randomness. Strikingly, the interference level (measured by coincidence) varied significantly along the chromosome in male meiosis and was correlated to the physical distance between COs. The significance of this finding on the relevance of current CO interference models is discussed.     

Physical mapping and identification of a candidate for the leaf rust resistance gene <Emphasis Type="Italic">Lr1</Emphasis> of wheat

Lr1 is a dominant leaf rust resistance gene located on chromosome 5DL of bread wheat and the wild species Aegilops tauschii. In this study, three polymorphic markers (WR001, WR002, and WR003) were developed from resistance gene analogs (RGAs) clustering around the Lr1 locus. Using these and other markers, Lr1 was mapped to a genetic interval of 0.79 cM in Ae. tauschii and 0.075 cM in wheat. The CAPS marker WR003, derived from LR1RGA1, co-segregated with Lr1 in both mapping populations of wheat and Ae. tauschii. For isolation of Lr1, two genomic BAC libraries (from Ae. tauschii and hexaploid wheat) were screened using the tightly flanking marker PSR567F and a set of nested primers derived from the conserved region of the RGA sequences. Approximately 400 kb BAC contig spanning the Lr1 locus was constructed. The LR1RGA1 encoding a CC-NBS-leucine-rich repeat (LRR) type of protein was the only one of the four RGAs at the Lr1 locus, which co-segregated with leaf rust resistance. Therefore, it represents a very good candidate for Lr1. The allelic sequences of LR1RGA1 from resistant and susceptible lines revealed a divergent DNA sequence block of ∼605 bp encoding the LRR repeats 9–15, whereas the rest of the sequences were mostly identical. Within this sequence block, the 48 non-synonymous changes resulted in 44 amino acid differences. This indicates that LR1RGA1 likely evolved through one or more recombination or gene conversion events with unknown genes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Chromosome‐level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing,Bionano and Hi‐C technology

Onychostoma macrolepis is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome‐level assembly of the O.macrolepis genome obtained from the integration of nanopore long‐read sequencing with physical maps produced using Bionano and Hi‐C technology. A total of 87.9 Gb of nanopore sequence provided approximately 100‐fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi‐C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein‐coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non‐coding RNAs, in the genome. Evolutionary analysis revealed that O. macrolepis diverged from common carp approximately 24.25 million years ago. The chromosomes of O. macrolepis showed an unambiguous correspondence to the chromosomes of zebrafish. The high‐quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of O. macrolepis.     

An integrated map of human 6q22.3-q24 including a 3-Mb high-resolution BAC/PAC contig encompassing a QTL for fetal hemoglobin

Genetic studies have previously assigned a quantitative trait locus (QTL) for hemoglobin F and F cells to a region of approximately 4 Mb between the markers D6S408 and D6S292 on chromosome 6q23. An initial yeast artificial chromosome contig of 13 clones spanning this region was generated. Further linkage analysis of an extended kindred refined the candidate interval to 1-2 cM, and key recombination events now place the QTL within a region of <800 kb. We describe a high-resolution bacterial clone contig spanning 3 Mb covering this critical region. The map consists of 223 bacterial artificial chromosome (BAC) and 100 P1 artificial chromosome (PAC) clones ordered by sequence-tagged site (STS) content and restriction fragment fingerprinting with a minimum tiling path of 22 BACs and 1 PAC. A total of 194 STSs map to this interval of 3 Mb, giving an average marker resolution of approximately one per 15 kb. About half of the markers were novel and were isolated in the present study, including three CA repeats and 13 single nucleotide polymorphisms. Altogether 24 expressed sequence tags, 6 of which are unique genes, have been mapped to the contig.     

De novo assembly of a chromosome‐level reference genome of red‐spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi‐C

The red‐spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and South‐East Asia and is a threatened species. The species is also considered a good model for studies of sex inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome‐level reference genome of E. akaara by taking advantage of long‐read single‐molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi‐C. A red‐spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96‐fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudochromosomes covering approximately 95.55% of the genome assembly with Hi‐C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 noncoding RNAs. Furthermore, combined with several RNA‐seq data sets, 23,808 (99.5%) genes were functionally annotated from a total of 23,923 predicted protein‐coding sequences. The high‐quality chromosome‐level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red‐spotted grouper in the future.     

Rapid evolutionary dynamics in a 2.8‐Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii

Prolamin and resistance gene families are important in wheat food use and in defense against pathogen attacks, respectively. To better understand the evolution of these multi‐gene families, the DNA sequence of a 2.8‐Mb genomic region, representing an 8.8 cM genetic interval and harboring multiple prolamin and resistance‐like gene families, was analyzed in the diploid grass Aegilops tauschii, the D‐genome donor of bread wheat. Comparison with orthologous regions from rice, Brachypodium, and sorghum showed that the Ae. tauschii region has undergone dramatic changes; it has acquired more than 80 non‐syntenic genes and only 13 ancestral genes are shared among these grass species. These non‐syntenic genes, including prolamin and resistance‐like genes, originated from various genomic regions and likely moved to their present locations via sequence evolution processes involving gene duplication and translocation. Local duplication of non‐syntenic genes contributed significantly to the expansion of gene families. Our analysis indicates that the insertion of prolamin‐related genes occurred prior to the separation of the Brachypodieae and Triticeae lineages. Unlike in Brachypodium, inserted prolamin genes have rapidly evolved and expanded to encode different classes of major seed storage proteins in Triticeae species. Phylogenetic analyses also showed that the multiple insertions of resistance‐like genes and subsequent differential expansion of each R gene family. The high frequency of non‐syntenic genes and rapid local gene evolution correlate with the high recombination rate in the 2.8‐Mb region with nine‐fold higher than the genome‐wide average. Our results demonstrate complex evolutionary dynamics in this agronomically important region of Triticeae species.     

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

During 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.     

Reduced Crossover Interference and Increased ZMM-Independent Recombination in the Absence of Tel1/ATM

Meiotic recombination involves the repair of double-strand break (DSB) precursors as crossovers (COs) or noncrossovers (NCOs). The proper number and distribution of COs is critical for successful chromosome segregation and formation of viable gametes. In budding yeast the majority of COs occurs through a pathway dependent on the ZMM proteins (Zip2-Zip3-Zip4-Spo16, Msh4-Msh5, Mer3), which form foci at CO-committed sites. Here we show that the DNA-damage-response kinase Tel1/ATM limits ZMM-independent recombination. By whole-genome mapping of recombination products, we find that lack of Tel1 results in higher recombination and reduced CO interference. Yet the number of Zip3 foci in tel1Δ cells is similar to wild type, and these foci show normal interference. Analysis of recombination in a tel1Δ zip3Δ double mutant indicates that COs are less dependent on Zip3 in the absence of Tel1. Together these results reveal that in the absence of Tel1, a significant proportion of COs occurs through a non-ZMM-dependent pathway, contributing to a CO landscape with poor interference. We also see a significant change in the distribution of all detectable recombination products in the absence of Tel1, Sgs1, Zip3, or Msh4, providing evidence for altered DSB distribution. These results support the previous finding that DSB interference depends on Tel1, and further suggest an additional level of DSB interference created through local repression of DSBs around CO-designated sites.     

Genetic and physical mapping of xa13, a recessive bacterial blight resistance gene in rice

 The recessive gene, xa13, confers resistance to Philippine race 6 (PXO99) of the bacterial blight pathogen Xanthomonas oryzae pv oryzae. Fine genetic mapping and physical mapping were conducted as initial steps in an effort to isolate the gene. Using nine selected DNA markers and two F₂ populations of 132 and 230 plants, xa13 was fine-mapped to a genomic region <4 cM on the long arm of rice chromosome 8, flanked by two RFLP markers, RG136 and R2027. Four DNA markers, RG136, R2027, S14003, and G1149, in the target region were used to identify bacterial artificial chromosome (BAC) clones potentially harboring the xa13 locus from a rice BAC library. A total of 11 BACs were identified, forming four separate contigs including a single-clone contig, 29I3, associated with the RG136 STS marker, the S14003 contig consisting of four clones (44F8, 41O2, 12A16, and 12F20), the G1149 contig with two clones, 23D11 and 21H18, and the R2027 contig consisting of four overlapping clones, 42C23, 30B5, 6B7 and 21H14. Genetic mapping indicated that the xa13 locus was contained in the R2027 contig. Chromosomal walking on the R2027 contig resulted in two more clones, 33C7 and 14L3. DNA fingerprinting showed that the six clones of the R2027 contig were overlapping. Clone 44F8 hybridized with a single fragment from the clone 14L3, integrating the R2027 and S14003 contigs into a single contig consisting of ten BAC clones with a total size of approximately 330 kb. The physical presence of the xa13 locus in the contig was determined by mapping the ends of the BAC inserts generated by TAIL-PCR. In an F₂ population of 230 plants, the BAC-end markers 42C23R and 6B7F flanked the xa13 locus. The probes 21H14F and 21H14R derived from BAC clone 21H14 were found to flank xa13 at a distance of 0.5 cM on either side, using a second F₂ population of 132 plants. Thus, genetic mapping indicated that the contig and the 96-kb clone, 21H14, contained the xa13 locus. Received: 15 August 1998 / Accepted: 29 September 1998     

Detailed Recombination Studies Along Chromosome 3B Provide New Insights on Crossover Distribution in Wheat (Triticum aestivum L.)

In wheat (Triticum aestivum L.), the crossover (CO) frequency increases gradually from the centromeres to the telomeres. However, little is known about the factors affecting both the distribution and the intensity of recombination along this gradient. To investigate this, we studied in detail the pattern of CO along chromosome 3B of bread wheat. A dense reference genetic map comprising 102 markers homogeneously distributed along the chromosome was compared to a physical deletion map. Most of the COs (90%) occurred in the distal subtelomeric regions that represent 40% of the chromosome. About 27% of the proximal regions surrounding the centromere showed a very weak CO frequency with only three COs found in the 752 gametes studied. Moreover, we observed a clear decrease of CO frequency on the distal region of the short arm. Finally, the intensity of interference was assessed for the first time in wheat using a Gamma model. The results showed m values of 1.2 for male recombination and 3.5 for female recombination, suggesting positive interference along wheat chromosome 3B.     

A whole genome sequence association study for puberty in a large Duroc × Erhualian F2 population

A large proportion of gilts and sows are culled from reproduction populations because of anestrus and pubertal reproductive failure. Selecting early onset of puberty gilts has a favorable effect on sows’ reproductivity. However, age at puberty is hard to be routinely measured in commercial herds. With molecular genetic predictors, identifying individuals that have a propensity for early onset of puberty can be simplified. We previously performed genome scanning and a genome‐wide association study for puberty in an F2 resource population using 183 microsatellites and 62 125 SNPs respectively. The detection power and resolution of identified quantitative trait loci were very low. Herein, we re‐sequenced 19 founders of the F2 resource population in high coverage, and whole genome sequences of F2 individuals were imputed to perform an association study for reproductive traits. A total of 2339 SNPs associated with pubertal reproductive failure were identified in the region of 30.94–40.74 Mb on SSC7, with the top one, positioned at 33.36 Mb, explaining 16% of the phenotypic variances. We improved the magnitude of the P‐value by 10E+5 to 10E+7 using the whole genome sequence rather than using low/middle density markers as in previous studies, and we narrowed down the QTL confidence interval to 5.25 Mb. Combining the annotation of gene function, RAB23 and BAK1 were perceived as the most compelling candidate genes. The identified loci may be useful in culling sows failing to show estrus by marker‐assisted selection to increase reproductive efficiency of swine herds.     

Chromosome‐level genome assembly of the predator Propylea japonica to understand its tolerance to insecticides and high temperatures

The ladybird beetle Propylea japonica is an important natural enemy in agro‐ecological systems. Studies on the strong tolerance of P. japonica to high temperatures and insecticides, and its population and phenotype diversity have recently increased. However, abundant genome resources for obtaining insights into stress‐resistance mechanisms and genetic intra‐species diversity for P. japonica are lacking. Here, we constructed the P. japonica genome maps using Pacific Bioscience (PacBio) and Illumina sequencing technologies. The genome size was 850.90 Mb with a contig N50 of 813.13 kb. The Hi‐C sequence data were used to upgrade draft genome assemblies; 4,777 contigs were assembled to 10 chromosomes; and the final draft genome assembly was 803.93 Mb with a contig N50 of 813.98 kb and a scaffold N50 of 100.34 Mb. Approximately 495.38 Mb of repeated sequences was annotated. The 18,018 protein‐coding genes were predicted, of which 95.78% were functionally annotated, and 1,407 genes were species‐specific. The phylogenetic analysis showed that P. japonica diverged from the ancestor of Anoplophora glabripennis and Tribolium castaneum ~ 236.21 million years ago. We detected that some important gene families involved in detoxification of pesticides and tolerance to heat stress were expanded in P. japonica, especially cytochrome P450 and Hsp70 genes. Overall, the high‐quality draft genome sequence of P. japonica will provide invaluable resource for understanding the molecular mechanisms of stress resistance and will facilitate the research on population genetics, evolution and phylogeny of Coccinellidae. This genome will also provide new avenues for conserving the diversity of predator insects.     

The pomegranate (Punica granatum L.) draft genome dissects genetic divergence between soft‐ and hard‐seeded cultivars

Complete and highly accurate reference genomes and gene annotations are indispensable for basic biological research and trait improvement of woody tree species. In this study, we integrated single‐molecule sequencing and high‐throughput chromosome conformation capture techniques to produce a high‐quality and long‐range contiguity chromosome‐scale genome assembly of the soft‐seeded pomegranate cultivar ‘Tunisia’. The genome covers 320.31 Mb (scaffold N50 = 39.96 Mb; contig N50 = 4.49 Mb) and includes 33 594 protein‐coding genes. We also resequenced 26 pomegranate varieties that varied regarding seed hardness. Comparative genomic analyses revealed many genetic differences between soft‐ and hard‐seeded pomegranate varieties. A set of selective loci containing SUC8‐like, SUC6, FoxO and MAPK were identified by the selective sweep analysis between hard‐ and soft‐seeded populations. An exceptionally large selective region (26.2 Mb) was identified on chromosome 1. Our assembled pomegranate genome is more complete than other currently available genome assemblies. Our results indicate that genomic variations and selective genes may have contributed to the genetic divergence between soft‐ and hard‐seeded pomegranate varieties.