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Safflower oil with high oleic is an important source of oil due to its oxidative stability and nutritional value as well as its industrial benefits. Identification of molecular markers associated with oil quality traits may aid in genotype selection in breeding efforts of safflower. To determine the genetic basis of seed oil, oleic acid, and linoleic acid content in safflower seeds, a recombinant inbred population was developed from a cross between Goldasht (low oleic line) and Mex 22–191 (high oleic line) by individual self-pollinated plants in each generation (from F2 to F9). Fatty acid components were detected by gas chromatography and subsequently analyzed by QTL analysis. The high variability in fatty acid composition was demonstrated and the first high-oleic safflower genotype was generated. A new linkage map with 69 AFLP and 45 ISSR polymorphic markers was made, covering 1472,441 cM of the safflower genome. A total of 63 individual QTLs and 238 epistatic QTLs, related to oil quality, were detected in 14 genomic regions. Some major QTLs with phenotypic variation greater than 10% were identified for the measured traits. These results demonstrate that major QTL may play an important role in increase the oleic acid of the genetic material used. Furthermore, the larger number of minor QTLs and epistatic QTLs, both of which have additive effects, indicates that the expression of these traits is also influenced by interactions between multiple genes. Our results provide additional genetic resources that can be used to precisely breed these traits in the future. [ABSTRACT FROM AUTHOR]

• This work represents the first-ever detailed multiple marker studies in Stevia. • QTL identification is the novelty of the work that will promote stevia breeding. • The QTL identified could be used in the mapping of genes responsible for rebaudioside-A. • Functional polymorphic markers will be useful in genetic dissection of traits. Stevia rebaudiana Bertoni, belonging to the family Asteraceae, is one of the most important perennial medicinal plants. It is used as a no-calorie sweetener therefore; mining of sweetening genes using molecular markers is a thrust area. In the present study combinations of markers were screened. Out of 170 RAPD, 26 ISSR, and 89 EST-SSR primers, it was observed that 36 RAPD, 10 ISSR, and 33 EST-SSR were found to be polymorphic. Using MAPMAKER/EXP version 3.0 b, four linkage groups were constructed spanning a distance of 927.3 cM with an average distance between loci of 16.29 cM. On QTL identification, a total of 53 locations were found for both trait 1 (rebaudioside-A) and trait 2 (stevioside). Among 53 QTL locations of trait 1, two major QTL were found for rebaudioside-A namely, in the marker interval of L67–L71 (ISSR HB-11)–(IISRS-3-L) in LG1 and the marker interval of L38–L40 (Sigma-5383–027)- (Sigma-5383-029) in LG3 at LOD of 2.5 and 2.7, respectively. The map constructed and QTL identified will greatly facilitate further genetic studies. It is hoped that this work will have a practical impact on the advancement of stevia breeding and genome analysis. [ABSTRACT FROM AUTHOR]

Genotyping‐by‐sequencing (GBS) is a widely used strategy for obtaining large numbers of genetic markers in model and non‐model organisms. In crop plants, GBS‐derived marker datasets are frequently used to perform quantitative trait locus (QTL) mapping. In some plant species, however, high heterozygosity and complex genome structure mean that researchers must use care in handling GBS data to conduct QTL mapping most effectively. Such outbred crops include most of the perennial grass and tree species used for bioenergy. To identify strategies for increasing accuracy and precision of QTL mapping using GBS data in outbred crops, we conducted an empirical study of SNP‐calling and genetic map‐building pipeline parameters in a Miscanthus sinensis population, and a complementary simulation study to estimate the relationship between genome‐wide error rate, read depth, and marker number. The bioenergy grass Miscanthus is an obligate outcrossing species with a recent (diploidized) whole‐genome duplication. For the study of empirical M. sinensis data, we compared two SNP‐calling methods (one non‐reference‐based and one reference‐based), a series of depth filters (12×, 20×, 30×, and 40×) and two map‐construction methods (i.e., marker ordering: linkage‐only and order‐corrected based on a reference genome). We found that correcting the order of markers on a linkage map by using a high‐quality reference genome improved QTL precision (shorter confidence intervals). For typical GBS datasets of between 1000 and 5000 markers to build a genetic map for biparental populations, a depth filter set at 30× to 40× applied to outbred populations provided a genome‐wide genotype‐calling error rate of less than 1%, improved accuracy of QTL point estimates and minimized type I errors for identifying QTL. Based on these results, we recommend using a reference genome to correct the marker order of genetic maps and a robust genotype depth filter to improve QTL mapping for outbred crops. [ABSTRACT FROM AUTHOR]

Sheath blight (ShB) is the most serious disease of rice (Oryza sativa L.), caused by the soil-borne fungus Rhizoctonia solani Kühn (R. solani). It poses a significant threat to global rice productivity, resulting in approximately 50% annual yield loss. Managing ShB is particularly challenging due to the broad host range of the pathogen, its necrotrophic nature, the emergence of new races, and the limited availability of highly resistant germplasm. In this study, we conducted QTL mapping using an F2 population derived from a cross between a partially resistant accession (IRGC81941A) of Oryza nivara and the susceptible rice cultivar Punjab rice 121 (PR121). Our analysis identified 29 QTLs for ShB resistance, collectively explaining a phenotypic variance ranging from 4.70 to 48.05%. Notably, a cluster of four QTLs (qRLH1.1, qRLH1.2, qRLH1.5, and qRLH1.8) on chromosome 1 consistently exhibit a resistant response against R. solani. These QTLs span from 0.096 to 420.1 Kb on the rice reference genome and contain several important genes, including Ser/Thr protein kinase, auxin-responsive protein, protease inhibitor/seed storage/LTP family protein, MLO domain-containing protein, disease-responsive protein, thaumatin-like protein, Avr9/Cf9-eliciting protein, and various transcription factors. Additionally, simple sequence repeats (SSR) markers RM212 and RM246 linked to these QTLs effectively distinguish resistant and susceptible rice cultivars, showing great promise for marker-assisted selection programs. Furthermore, our study identified pre-breeding lines in the advanced backcrossed population that exhibited superior agronomic traits and sheath blight resistance compared to the recurrent parent. These promising lines hold significant potential for enhancing the sheath blight resistance in elite cultivars through targeted improvement efforts. [ABSTRACT FROM AUTHOR]

Soybean is a major crop in the world and an essential source for minerals, including iron (Fe) and zin (Zn). Deficiency of Fe and Zn in soil and soybean plants result in yield loss and poor seed nutritional qualities. Information on genomic regions and candidate genes controlling seed Fe and Zn accumulation in soybean seed is limited. Therefore, The objective of this research was to identify genetic regions, known as quantitative trait loci (QTL), and candidate genes that control the accumulation of Fe and Zn in soybean mature seeds. A 'Forrest' by 'Williams 82' (F × W82) recombinant inbred line (RIL) population (n = 306) was used and genotyped using a total of 5405 single nucleotides polymorphism (SNP) markers using Infinium SNP6K BeadChips. A two-year experiment was conducted across two environments: North Carolina in 2018 (NC) and Illinois in 2020 (IL). Only QTL with LOD scores ≥ 2.5, as identified by the composite interval mapping (CIM) method, are reported here. In total, 6 QTL were identified for seed Fe; specifically, 3 QTL (qFe-01-[NC-2018], qFe-02-[NC-2018], and qFe-03-[NC-2018]) were located on chromosomes 1, 2, and 6, respectively, in the NC environment, and 3 QTL (qFe-01-[IL-2020], qFe-02-[IL-2020], and qFe-03-[IL-2020]) were positioned on chromosomes 1, 2, and 12, respectively, in the IL environment. A total of 6 QTL associated with seed Zn were also identified; 4 QTL (qZn-01-[NC-2018]; qZn-02-[NC-2018]; qZn-03-[NC-2018]; and qZn-04-[NC-2018]), respectively on Chr 2, 3, 7, and 19 in NC; and 2 QTL (qZn-01-[IL-2020] and qZn-02-[IL-2020]), respectively, on Chr 5 and 8 in IL. Several functional genes encode Fe- and Zn-proteins, transcription factors, proteins-zinc finger motifs (involved in DNA binding and transcriptional regulation; crosstalk between the regulatory pathways of Zn and Fe transporters) were identified and located within the QTL interval. To our knowledge, and based on the literature available, the QTL identified here on Chr 2 and Chr 6 are novel and were not previously identified. This current research provides a new knowledge of the genetic basis of seed Fe and Zn and the markers associated with QTL. The QTL identified here will contribute to efficient marker assisted selection for higher Fe and Zn content in soybean seeds. The candidate genes and metal-responsive transcription factors may coordinate the expression of both Zn and Fe transporters in response to changes in metal availability, providing new knowledge on minerals uptake and transport mechanisms, allowing for possible genetic engineering application. [ABSTRACT FROM AUTHOR]

Linkage maps are essential for genetic mapping of phenotypic traits, gene map-based cloning, and marker-assisted selection in breeding applications. Construction of a high-quality saturated map requires high-quality genotypic data on a large number of molecular markers. Errors in genotyping cannot be completely avoided, no matter what platform is used. When genotyping error reaches a threshold level, it will seriously affect the accuracy of the constructed map and the reliability of consequent genetic studies. In this study, repeated genotyping of two recombinant inbred line (RIL) populations derived from crosses Yangxiaomai × Zhongyou 9507 and Jingshuang 16 × Bainong 64 was used to investigate the effect of genotyping errors on linkage map construction. Inconsistent data points between the two replications were regarded as genotyping errors, which were classified into three types. Genotyping errors were treated as missing values, and therefore the non-erroneous data set was generated. Firstly, linkage maps were constructed using the two replicates as well as the non-erroneous data set. Secondly, error correction methods implemented in software packages QTL IciMapping (EC) and Genotype-Corrector (GC) were applied to the two replicates. Linkage maps were therefore constructed based on the corrected genotypes and then compared with those from the non-erroneous data set. Simulation study was performed by considering different levels of genotyping errors to investigate the impact of errors and the accuracy of error correction methods. Results indicated that map length and marker order differed among the two replicates and the non-erroneous data sets in both RIL populations. For both actual and simulated populations, map length was expanded as the increase in error rate, and the correlation coefficient between linkage and physical maps became lower. Map quality can be improved by repeated genotyping and error correction algorithm. When it is impossible to genotype the whole mapping population repeatedly, 30% would be recommended in repeated genotyping. The EC method had a much lower false positive rate than did the GC method under different error rates. This study systematically expounded the impact of genotyping errors on linkage analysis, providing potential guidelines for improving the accuracy of linkage maps in the presence of genotyping errors. [ABSTRACT FROM AUTHOR]

Crop yield is a complex phenomenon, controlled by several genes, each contributing to the overall phenotypic expression; which is affected by environment and genotype x environment interactions. Identifying and mapping quantitative trait loci (QTLs), make tracing these traits during breeding possible and easy. The objective of this study was to identify QTLs associated with chickpea (Cicer arietinum L.) grain yield and its associated traits, under drought stress. The experiment was conducted using 188 F3:5 genotypes from ICCV 05107 x ICCV 94954 crosses. Genotypic data were from 49 polymorphic simple sequence repeat (SSR) markers; while phenotypic data were obtained from a field evaluation designed in a 19 x 10 alpha lattice. The study was replicated thrice on three sites, namely at Koibatek Agricultural Training Centre, Muserech; and at the Kenya Agricultural Research and Livestock Organisation, Marigat. Eight QTLs were mapped on a linkage map spanning a total length of 335.04 cM, with varying phenotypic variation expression (PVE%). These QTLs include, one each for days to maturity, 100-seed weight, and two each for above-ground biomass, harvest index, and grain yield. Five major QTLs having PVE ranging from 10.37 to 32.39%, were identified for days to maturity, 100-seed weight above-ground biomass, harvest index (HI), and grain yield. Four of the eight QTLs were mapped on linkage group 4 (LG4); days to maturity, 2 for above-ground biomass, and grain yield. The QTLs mapped are useful in genomic-assisted breeding for chickpea yield improvement. However, there is a need for marker saturation on LGs and specific genes identified for effective marker-assisted breeding. [ABSTRACT FROM AUTHOR]

The reinvention of potato, from a tetraploid clonal crop into a diploid seed-based hybrid crop, requires insight in the mutational load, recombination landscape, and the genetic basis of fertility. Genomics-based breeding and QTL discovery rely on efficient genotyping strategies such as skim sequencing, to gather genotypic information. The application of skim sequencing to full-sib population of non-inbred parents remains challenging. Here, we report on an R implementation of the OutcrossSeq pipeline for diploids. We applied this pipeline to a large diploid skim sequenced potato population. We used the resulting bin-markers for the construction of high-density parent specific linkage maps, highlighting variation in parental recombination rate and structural variations. We subsequently explored transmission ratio distortion and non-independent assortment of alleles, indicative of large-effect deleterious mutations. Finally, we identified QTLs for seedling tuber yield in pots and pollen shed. This study showcases the range of genetic analyses, from marker inference, identification of transmission ratio distortion, and linkage map construction to QTL mapping, resulting in new insights that contribute to breeding diploid potato. [ABSTRACT FROM AUTHOR]

A large seed mutant, TG 89 having a 76.7% increment in hundred kernel weight in comparison to its parent TG 26, was isolated from an electron beam-induced mutagenized population. Studies based on environmental scanning electron microscopy of both parent and mutant revealed that the mutant seed cotyledon had significantly bigger cell size than parent. A mapping population with 122 F2 plants derived from the mutant and a distant normal seed genotype (ICGV 15007) was utilized to map the QTL associated with higher HKW. Bulk segregant analysis revealed putative association of three markers with this mutant large seed trait. Further, genotyping of F2 individuals with polymorphic markers detected 14 linkage groups with a map distance of 1053 cM. QTL analysis revealed a significant additive major QTL for the mutant large seed trait on linkage group A05 explaining 12.7% phenotypic variation for the seed size. This QTL was located between flanking markers AhTE333 and AhTE810 having a map interval of 4.7 cM which corresponds to 90.65 to 107.24 Mbp in A05 chromosome, respectively. Within this genomic fragment, an ortholog of the BIG SEEDS 1 gene was found at 102,476,137 bp. Real-time PCR revealed down-regulation of this BIG SEEDS 1 gene in the mutant indicating a loss of function mutation giving rise to a large seed phenotype. This QTL was validated in 11 advanced breeding lines having large seed size from this mutant but with varied genetic backgrounds. This validation showcased a highly promising selection accuracy of 90.9% for the marker-assisted selection. [ABSTRACT FROM AUTHOR]

Shiitake mushroom (Lentinula edodes) is one of the most popular and widely cultivated mushrooms, especially in East Asia. Temperature is the critical factor affecting fruiting body induction. Due to climate change and increasing fuel costs, there is a growing demand for breeding L. edodes strains that fruit at higher temperatures. This study constructed a linkage map using 94 single spore isolates (SSIs) from the hybrid strain MCR 487 derived from crossing the high-temperature type (H-type) strain KRCF 1097 and the low to medium-temperature type (LM-type) strain KRCF 1101. Quantitative trait loci (QTLs) associated with higher-temperature fruiting ability were analyzed using 92 dikaryotic strains obtained from crossing SSIs from MCR 487 with the L-type strain KRCF 1098SS-2. Four QTLs (qTF1-4) controlling temperature for fruiting body induction were identified on the linkage map. Specific DNA marker was developed based on the sequence of the H-type qTF1, enabling the selection of strains capable of fruiting at higher temperatures. This study demonstrates that genome sequencing and QTL analysis can be used to obtain parental strains for breeding L. edodes strains suited for higher temperature cultivation, offering promising prospects for future breeding strategies. [ABSTRACT FROM AUTHOR]

The evolution of azole resistance in fungal pathogens presents a major challenge in both crop production and human health. Apple orchards across the world are faced with the emergence of azole fungicide resistance in the apple scab pathogen Venturia inaequalis. Target site point mutations observed in this fungus to date cannot fully explain the reduction in sensitivity to azole fungicides. Here, polygenic resistance to tebuconazole was studied across a population of V. inaequalis. Genotyping by sequencing allowed Quantitative Trait Loci (QTLs) mapping to identify the genetic components controlling this fungicide resistance. Dose-dependent genetic resistance was identified, with distinct genetic components contributing to fungicide resistance at different exposure levels. A QTL within linkage group seven explained 65% of the variation in the effective dose required to reduce growth by 50% (ED50). This locus was also involved in resistance at lower fungicide doses (ED10). A second QTL in linkage group one was associated with dose-dependent resistance, explaining 34% of variation at low fungicide doses (ED10), but did not contribute to resistance at higher doses (ED50 and ED90). Within QTL regions, non-synonymous mutations were observed in several ATP-Binding Cassette and Major Facilitator SuperFamily transporter genes. These findings provide insight into the mechanisms of fungicide resistance that have evolved in horticultural pathogens. Identification of resistance gene candidates supports the development of molecular diagnostics to inform management practices. [ABSTRACT FROM AUTHOR]

Horsegram (Macrotyloma uniflorum) - an important, self-pollinated food legume, however due to limited genomic and genetic resources the genetic improvement could not be achieved as compare to other major legumes. Our work aims at finding novel microsatellite markers and their use for the construction of a linkage map from 157 individuals of F9 recombinant inbred lines (RILs) of horsegram. The determinate growth habit and plant height are important traits for its suitability for different cropping systems. The genotypic data were generated by screening 2 395 molecular markers, of which 600 (25.05 %) polymorphic markers were selected. Two-hundred eighty-seven markers were mapped on ten linkage groups (LGs) at a log of odds (LOD) of 3.5 straddling 796.76 cM with 2.78 cM of marker density. For the identification of the quantitative trait loci (QTLs), the phenotypic data recorded on the RILs for the plant height and growth habit were analysed using the statistical tools JoinMap® and Windows QTL cartographer, based on the composite interval mapping (CIM) technique. Across the ten linkage groups, we detected four QTLs (LOD ≥ 2.5) for four traits. All the traits were major QTLs as indicated by the percentage of phenotypic variance (PVE) (≥ 10%) that ranged from 13.5% to 40.3%, therefore, this is very important information which can be used in marker-assisted selection (MAS). The present genomic information generated in this orphan crop, thus, provides the base for genetic improvements by devising molecular breeding strategies. [ABSTRACT FROM AUTHOR]

Obligate parthenogenesis (OP) is often thought to evolve by disruption of reductional meiosis and suppression of crossover recombination. In the crustacean Daphnia pulex , OP lineages, which have evolved from cyclical parthenogenetic (CP) ancestors, occasionally produce males that are capable of reductional meiosis. Here, by constructing high-density linkage maps, we find that these males show only slightly and nonsignificantly reduced recombination rates compared to CP males and females. Both meiosis disruption and recombination suppression are therefore sex-limited (or partly so), which speaks against the evolution of OP by disruption of a gene that is essential for meiosis or recombination in both sexes. The findings may be explained by female-limited action of genes that suppress recombination, but previously identified candidate genes are known to be expressed in both sexes. Alternatively, and equally consistent with the data, OP might have evolved through a reuse of the parthenogenesis pathways already present in CP and through their extension to all events of oogenesis. The causal mutations for the CP to OP transition may therefore include mutations in genes involved in oogenesis regulation and may not necessarily be restricted to genes of the "meiosis toolkit." More generally, our study emphasizes that there are many ways to achieve asexuality, and elucidating the possible mechanisms is key to ultimately identify the genes and traits involved. [ABSTRACT FROM AUTHOR]

Background: For Asian seabass (Lates calcarifer, Bloch 1790) cultured at sea cages various aquatic pathogens, complex environmental and stress factors are considered as leading causes of disease, causing tens of millions of dollars of annual economic losses. Over the years, we conducted farm-based challenges by exposing Asian seabass juveniles to complex natural environmental conditions. In one of these challenges, we collected a total of 1,250 fish classified as either 'sensitive' or 'robust' individuals during the 28-day observation period. Results: We constructed a high-resolution linkage map with 3,089 SNPs for Asian seabass using the double digest Restriction-site Associated DNA (ddRAD) technology and a performed a search for Quantitative Trait Loci (QTL) associated with robustness. The search detected a major genome-wide significant QTL for increased robustness in pathogen-infected marine environment on linkage group 11 (ASB_LG11; 88.9 cM to 93.6 cM) with phenotypic variation explained of 81.0%. The QTL was positioned within a > 800 kb genomic region located at the tip of chromosome ASB_LG11 with two Single Nucleotide Polymorphism markers, R1-38468 and R1-61252, located near to the two ends of the QTL. When the R1-61252 marker was validated experimentally in a different mass cross population, it showed a statistically significant association with increased robustness. The majority of thirty-six potential candidate genes located within the QTL have known functions related to innate immunity, stress response or disease. By utilizing this ddRAD-based map, we detected five mis-assemblies corresponding to four chromosomes, namely ASB_LG8, ASB_LG9, ASB_LG15 and ASB_LG20, in the current Asian seabass reference genome assembly. Conclusion: According to our knowledge, the QTL associated with increased robustness is the first such finding from a tropical fish species. Depending on further validation in other stocks and populations, it might be potentially useful for selecting robust Asian seabass lines in selection programs. [ABSTRACT FROM AUTHOR]

Simple Summary: Although lentil is not as popular as other legumes, it is a climate-resilient legume crop because of its high protein content, nitrogen fixation, and abiotic stress tolerance ability. Even though it can be grown on almost every continent and is distributed globally, the use of existing genetic diversity in marker-assisted selection is still limited. In this study, novel SSR markers needed in lentil were identified using a next-generation sequencing approach. In this study, we created a ready-to-use SSR library for genetic diversity studies and breeding and evaluated the effectiveness of the obtained SSR markers in a recombinant inbred line (RIL) population. Simple sequence repeats (SSRs) are highly versatile markers in genetic diversity analysis and plant breeding, making them widely applicable. They hold potential in lentil (Lens culinaris) breeding for genetic diversity analysis, marker-assisted selection (MAS), and linkage mapping. However, the availability and diversity of SSR markers in lentil is limited. We used next-generation sequencing (NGS) technology to develop SSR markers in lentil. NGS allowed us to identify regions of the lentil genome that contained SSRs. Illumina Hiseq-2000 sequencing of the lentil genotype "Karacadağ" resulted in 1,727,734 sequence reads comprising more than 48,390 Mb, and contigs were mined for SSRs, resulting in the identification of a total of 8697 SSR motifs. Among these, dinucleotide repeats were the most abundant (53.38%), followed by trinucleotides (30.38%), hexanucleotides (6.96%), tetranucleotides (6.59%), and pentanucleotides (3.19%). The most frequent repeat in dinucleotides was the TC (21.80%), followed by the GA (17.60%). A total of 2000 primer pairs were designed from these motifs, and 458 SSR markers were validated following their amplified PCR products. A linkage map was constructed using these new SSRs with high linkage disequilibrium (209) and previously known SSRs (11). The highest number of SSR markers (43) was obtained in LG2, while the lowest number of SSR markers (19) was obtained in LG7. The longest linkage group (LG) was LG2 (86.84 cM), whereas the shortest linkage group was LG7 (53.46 cM). The average length between markers ranged from 1.86 cM in LG1 to 2.81 cM in LG7, and the map density was 2.16 cM. The developed SSRs and created linkage map may provide useful information and offer a new library for genetic diversity analyses, linkage mapping studies, and lentil breeding programs. [ABSTRACT FROM AUTHOR]

The silkworm (Bombyx mori) is an important lepidopteran model insect and an industrial domestic animal traditionally used for silk production. Here, we report the genome assembly of an improved Japanese strain Nichi01, in which the cocoon yield is comparable to that of commercial silkworm strains. The integration of PacBio Sequel II long-read and ddRAD-seq-based high-density genetic linkage map achieved the highest quality genome assembly of silkworms to date; 22 of the 28 pseudomolecules contained telomeric repeats at both ends, and only four gaps were present in the assembly. A total of 452 Mbp of the assembly with an N50 of 16.614 Mbp covered 99.3% of the complete orthologs of the lepidopteran core genes. Although the genome sequence of Nichi01 and that of the previously reported low-yielding tropical strain p50T assured their accuracy in most regions, we corrected several regions, misassembled in p50T, in our assembly. A total of 18,397 proteins were predicted using over 95 Gb of mRNA-seq derived from 10 different organs, covering 96.9% of the complete orthologs of the lepidopteran core genes. The final assembly and annotation files are available in KAIKObase (https://kaikobase.dna.affrc.go.jp/index.html) along with a genome browser and BLAST searching service, which would facilitate further studies and the breeding of silkworms and other insects. [ABSTRACT FROM AUTHOR]

Background: Sex determination occurs across animal species, but most of our knowledge about its mechanisms comes from only a handful of bilaterian taxa. This limits our ability to infer the evolutionary history of sex determination within animals. Results: In this study, we generated a linkage map of the genome of the colonial cnidarian Hydractinia symbiolongicarpus and used it to demonstrate that this species has an XX/XY sex determination system. We demonstrate that the X and Y chromosomes have pseudoautosomal and non-recombining regions. We then use the linkage map and a method based on the depth of sequencing coverage to identify genes encoded in the non-recombining region and show that many of them have male gonad-specific expression. In addition, we demonstrate that recombination rates are enhanced in the female genome and that the haploid chromosome number in Hydractinia is n = 15. Conclusions: These findings establish Hydractinia as a tractable non-bilaterian model system for the study of sex determination and the evolution of sex chromosomes. [ABSTRACT FROM AUTHOR]

Simple Summary: The California condor is a critically endangered representative of New World vultures maintained under restoration and reintroduction programs. Within a California condor genome research project, we made a preliminary step toward a genetic linage map for this iconic bird species. The respective linkage data were generated using a panel of 121 condors. The condors were genotyped for 123 polymorphic microsatellite markers. The condor genotyping and mapping results are a useful addition to the previously obtained physical and cytogenetic maps and can be further utilized in condor genome sequence assembly. The development of a linkage map is an important component for promoting genetic and genomic studies in California condors, an endangered New World vulture species. Using a set of designed anonymous microsatellite markers, we genotyped a reference condor population involving 121 individuals. After marker validation and genotype filtering, the genetic linkage analysis was performed using 123 microsatellite loci. This resulted in the identification of 15 linkage groups/subgroups that formed a first-generation condor genetic map, while no markers linked to a lethal chondrodystrophy mutation were found. A panel of polymorphic markers that is instrumental in molecular parentage diagnostics and other genetic studies in the California condor was selected. Further condor conservation genomics research will be focused on updating the linkage map and integrating it with cytogenetic and BAC-based physical maps and ultimately with the genome sequence assembly. [ABSTRACT FROM AUTHOR]

BACKGROUND: Deficiency of Zn is a major soil constraint in rice plant growth and yield. Edaphic factors such as Zn deficiency in soil in relation to plant performance are still poorly understood. Here, we report promising quantitative trait loci (QTL) conferring tolerance to Zn deficiency, which were identified through biparental mapping. The experiment was conducted using the 236 F7 recombinant inbred line mapping population derived from the cross of Kinandang Patong (Zn deficiency sensitive) and A69‐1 (Zn deficiency tolerant). RESULTS: A total of six QTLs (qLB‐2B, qLB‐4B, qPM‐4B, qPM‐6B, qRZC‐4B, qSZC‐4B) on chromosomes 2, 4 and 6 were identified for environment 1, whereas five QTLs (qLB‐2 N, qLB‐4 N, qPM‐4 N, qRZC‐4 N, qSZC‐4 N) on chromosomes 2 and 4 were detected for environment 2. Among these, five major (51.30, 48.70, 28.60, 56.00, 52.00 > 10 R2) and one minor (5.40 < 10 R2) QTLs for environment 1 and four major (51.48, 50.20, 53.00, 48.00 > 10 R2) and one minor (4.44 < 10) QTLs for environment 2 for Zn deficiency tolerance with a logarithm of odd threshold value higher than 3 were identified. The QTLs (qLB‐4B, qPM‐4B, qRZC‐4B, qSZC‐4B, qLB‐4 N, qPM‐4 N, qRZC‐4 N, qSZC‐4 N) for leaf bronzing, plant mortality root zinc concentration and shoot zinc concentration identified on chromosome 4 were found to be the most promising and highly reproducible across the locations that explained phenotypic variation from 48.00% to 56.00% with the same marker interval RM6748–RM303. CONCLUSION: The new QTLs and its linked markers identified in the present study can be utilized for Zn deficiency tolerance in elite cultivars using marker‐assisted backcrossing. © 2022 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Recombination strongly impacts sequence evolution by affecting the extent of linkage and the efficiency of selection. Here, we study recombination over the Z chromosome in great reed warblers (Acrocephalus arundinaceus) using pedigree‐based linkage mapping. This species has extended Z and W chromosomes ("neo‐sex chromosomes") formed by a fusion between a part of chromosome 4A and the ancestral sex chromosomes, which provides a unique opportunity to assess recombination and sequence evolution in sex‐linked regions of different ages. We assembled an 87.54 Mbp and 90.19 cM large Z with a small pseudoautosomal region (0.89 Mbp) at one end and the fused Chr4A‐part at the other end of the chromosome. A prominent feature in our data was an extreme variation in male recombination rate along Z with high values at both chromosome ends, but an apparent lack of recombination over a substantial central section, covering 78% of the chromosome. The nonrecombining region showed a drastic loss of genetic diversity and accumulation of repeats compared to the recombining parts. Thus, our data emphasize a key role of recombination in affecting local levels of polymorphism. Nonetheless, the evolutionary rate of genes (dN/dS) did not differ between high and low recombining regions, suggesting that the efficiency of selection on protein‐coding sequences can be maintained also at very low levels of recombination. Finally, the Chr4A‐derived part showed a similar recombination rate as the part of the ancestral Z that did recombine, but its sequence characteristics reflected both its previous autosomal, and current Z‐linked, recombination patterns. [ABSTRACT FROM AUTHOR]

The role of recombination in genome evolution has long been studied in theory, but until recently empirical investigations had been limited to a small number of model species. Here, we compare the recombination landscape and genome collinearity between two populations of the Atlantic silverside (Menidia menidia), a small fish distributed across the steep latitudinal climate gradient of the North American Atlantic coast. We constructed separate linkage maps for locally adapted populations from New York and Georgia and their interpopulation laboratory cross. First, we used one of the linkage maps to improve the current silverside genome assembly by anchoring three large unplaced scaffolds to two chromosomes. Second, we estimated sex‐specific recombination rates, finding 2.3‐fold higher recombination rates in females than males—one of the most extreme examples of heterochiasmy in a fish. While recombination occurs relatively evenly across female chromosomes, it is restricted to only the terminal ends of male chromosomes. Furthermore, comparisons of female linkage maps revealed suppressed recombination along several massive chromosomal inversions spanning nearly 16% of the genome. These inversions segregate between locally adapted populations and coincide near perfectly with blocks of highly elevated genomic differentiation between wild populations. Finally, we discerned significantly higher recombination rates across chromosomes in the northern population compared to the southern. In addition to providing valuable resources for ongoing evolutionary and comparative genomic studies, our findings represent a striking example of structural variation that impacts recombination between adaptively divergent populations, providing empirical support for theorized genomic mechanisms facilitating adaptation despite gene flow. [ABSTRACT FROM AUTHOR]

Within the genus Salix, there are approximately 350 species native primarily to the northern hemisphere and adapted to a wide range of habitats. This diversity can be exploited to mine novel alleles conferring variation important for production as a bioenergy crop, but also to identify evolutionarily important genes, such as those involved in sex determination. To leverage this diversity, we created a mapping population by crossing 6 Salix species (Salix viminalis, Salix suchowensis, Salix integra, Salix koriyanagi, Salix udensis, and Salix alberti) to common male and female Salix purpurea parents. Each family was genotyped via genotyping-by-sequencing and assessed for kinship and population structure as well as the construction of 16 backcross linkage maps to be used as a genetic resource for breeding and selection. Analyses of population structure resolved both the parents and F1 progeny to their respective phylogenetic section and indicated that the S. alberti parent was misidentified and was most likely S.suchowensis. Sex determining regions were identified on Salix chromosome 15 in the female-informative maps for seven of the eight families indicating that these species share a common female heterogametic ZW sex system. The eighth family, S. integra x S. purpurea, was entirely female and had a truncated chromosome 15. Beyond sex determination, the Salix F1 hybrid common parent population (Salix F1 HCP) introduced here will be useful in characterizing genetic factors underlying complex traits, aid in marker-assisted selection, and support genome assemblies for this promising bioenergy crop. [ABSTRACT FROM AUTHOR]

Foxtail millet (Setaria italica) is an ideal model of genetic system for functional genomics of the Panicoideae crop. Identification of QTL responsible for morpho-agronomic and yield-related traits facilitates dissection of genetic control and breeding in cereal crops. Here, based on a Yugu1 × Longgu7 RIL population and genome-wide resequencing data, an updated linkage map harboring 2297 bin and 74 SSR markers was constructed, spanning 1315.1 cM with an average distance of 0.56 cM between adjacent markers. A total of 221 QTL for 17 morpho-agronomic and yield-related traits explaining 5.5 ~ 36% of phenotypic variation were identified across multi-environments. Of these, 109 QTL were detected in two to nine environments, including the most stable qLMS6.1 harboring a promising candidate gene Seita.6G250500, of which 70 were repeatedly identified in different trials in the same geographic location, suggesting that foxtail millet has more identical genetic modules under the similar ecological environment. One hundred-thirty QTL with overlapping intervals formed 22 QTL clusters. Furthermore, six superior recombinant inbred lines, RIL35, RIL48, RIL77, RIL80, RIL115 and RIL125 with transgressive inheritance and enrichment of favorable alleles in plant height, tiller, panicle morphology and yield related-traits were screened by hierarchical cluster. These identified QTL, QTL clusters and superior lines lay ground for further gene-trait association studies and breeding practice in foxtail millet. [ABSTRACT FROM AUTHOR]

Genetic linkage maps based on single nucleotide polymorphisms (SNPs) represent an essential tool for a variety of genomic analyses. Today, next-generation sequencing (NGS) enables rapid genotyping of different mapping populations based on thousands of SNPs and the construction of highly saturated linkage maps. Nevertheless, missing data in the genotyping of the parental lines creates a bottleneck that determines the number of SNPs that can be used for the linkage map. As a proof of concept, a highly saturated genetic linkage map was constructed using the imputed genotypic data of a recombinant inbred line (RIL) population and the limited genotypic information of its parental lines. Two ABH genotype files were created from a pseudo-parental genotypic data set that includes all the SNPs present in the RIL population. In the first ABH file pseudo-parental 1 was considered parental A, while in the second pseudo-parental 1 was considered parental B. These two duplicate ABH genotype files were merged by chromosome and subjected to linkage map analysis. Since the ABH data were duplicated, two mirrored linkage groups were generated per chromosome. The correct linkage map was identified and selected based on the partial genotypic data of the parental lines. This strategy was effective for constructing a highly saturated linkage map of 33,421 SNPs based on the genotyping of 205 RILs and a limited number of 100 SNPs present in the parental lines. This strategy enables the use of all the NGS SNP data obtained from a low-coverage sequencing experiment in the mapping population. [ABSTRACT FROM AUTHOR]

Miscanthus is a perennial rhizomatous grass belonging to Andropogoneae, which is now used as lignocellulosic biomass crop. Miscanthus has a short history of domestication, so further breeding effort for improved biomass production is needed. Flowering plays a critical role in controlling vegetative growth and physiology of plant, so this study focused on finding quantitative trait locus controlling flowering of Miscanthus for use in marker assisted breeding. A cross-pollinated M. sinensis F 1 population consisted of 278 progenies was produced, transplanted to the field and assessed in their flowering traits. Julian dates of flag leaf extension, first heading, half heading, first flowering, and half flowering were assessed in 2019, the third year after transplanting when Miscanthus was well established. The average Julian dates of the flowering traits were 198±9, 224±14, 233±14, 239±15 and 253±12, respectively, and showed a proximal normal distribution. Genotype by sequencing conducted by Illumina-hiseq using leaf DNA samples revealed the genetic map consisted of 1988 SNPs with average distance of 1.35 cM. Nine QTLs controlling flowering were detected exceeded 60% of LOD score threshold. These QTLs were neighboring 16 SNP markers, 5 of which were contained in known functional genes including RGL2 (gibberellin pathway regulation). Genetic map and marker information acquired through this study, including either annotated or not annotated markers, are expected to help understand and help breeding new Miscanthus in the future with desired flowering. • Five flowering traits were closely related to each other. • A dense linkage map of 1988 SNPs within 2663 cM was constructed by NGS and reference mapping for Miscanthus sinensis. • Nine QTLs and neighboring 16 SNPs were discovered to control flowering traits. • One common SNP associated with 3 QTLs located at linkage group 7 newly discovered was related to all five flowering traits. [ABSTRACT FROM AUTHOR]

Genome sequencing methods and assembly tools have improved dramatically since the 2013 publication of draft genome assemblies for the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae). We conducted proximity ligation library sequencing and scaffolding to improve contiguity, and then used linkage mapping and recent bioinformatic tools for correction and further improvement. The new assemblies have dramatically improved contiguity and gaps compared to the originals: N50 values increased 26‐ to 36‐fold, and the number of gaps were reduced by half. Ninety per cent of the content of the assemblies is now contained in 12 and 11 scaffolds for the female and male assemblies, respectively. Based on linkage mapping information, the 12 largest scaffolds in both assemblies represent all 11 autosomal chromosomes and the neo‐X chromosome. These assemblies now have nearly chromosome‐sized scaffolds and will be instrumental for studying genomic architecture, chromosome evolution, population genomics, functional genomics, and adaptation in this and other pest insects. We also identified regions in two chromosomes, including the ancestral‐X portion of the neo‐X chromosome, with elevated differentiation between northern and southern Canadian populations. [ABSTRACT FROM AUTHOR]

The number and placement of meiotic crossover events during meiosis have important implications for the fidelity of chromosome segregation as well as patterns of inheritance. Despite the functional importance of recombination, recombination landscapes vary widely among and within species, and this can have a strong impact on evolutionary processes. A good knowledge of recombination landscapes is important for model systems in evolutionary and ecological genetics, since it can improve interpretation of genomic patterns of differentiation and genome evolution, and provides an important starting point for understanding the causes and consequences of recombination rate variation. Arabidopsis arenosa is a powerful evolutionary genetic model for studying the molecular basis of adaptation and recombination rate evolution. Here, we generate genetic maps for 2 diploid A. arenosa individuals from distinct genetic lineages where we have prior knowledge that meiotic genes show evidence of selection. We complement the genetic maps with cytological approaches to map and quantify recombination rates, and test the idea that these populations might have distinct patterns of recombination. We explore how recombination differs at the level of populations, individuals, sexes and genomic regions. We show that the positioning of crossovers along a chromosome correlates with their number, presumably a consequence of crossover interference, and discuss how this effect can cause differences in recombination landscape among sexes or species. We identify several instances of female segregation distortion. We found that averaged genome-wide recombination rate is lower and sex differences subtler in A. arenosa than in Arabidopsis thaliana. [ABSTRACT FROM AUTHOR]

Growth directly influences production rate and therefore is one of the most important and well-studied traits in animal breeding. However, understanding the genetic basis of growth has been hindered by its typically complex polygenic architecture. Here, we performed quantitative trait locus mapping and genome-wide association studies for 10 growth traits that were observed over 2 years in 1,100 F1 captive-bred trevally (Pseudocaranx georgianus). We constructed the first high-density linkage map for trevally, which included 19,861 single nucleotide polymorphism markers, and discovered 8 quantitative trait loci for height, length, and weight on linkage groups 3, 14, and 18. Using genome-wide association studies, we further identified 113 single nucleotide polymorphism-trait associations, uncovering 10 genetic hot spots involved in growth. Two of the markers found in the genome-wide association studies colocated with the quantitative trait loci previously mentioned, demonstrating that combining quantitative trait locus mapping and genome-wide association studies represents a powerful approach for the identification and validation of loci controlling complex traits. This is the first study of its kind for trevally. Our findings provide important insights into the genetic architecture of growth in this species and supply a basis for fine mapping quantitative trait loci, genomic selection, and further detailed functional analysis of the genes underlying growth in trevally. [ABSTRACT FROM AUTHOR]

Almond is one of the most important nut crops in Turkey. Simple sequence repeat (SSR)‐based linkage maps are very reliable in constructing linkage maps due to the co‐dominant and highly reproducible nature of the SSR markers. The objective of this study was to construct well‐saturated, SSR‐based genetic linkage maps using 'Gulcan‐2 × Lauranne' and 'Guara × Nurlu' F1 populations and to identify QTLs related to the flower colour, stigma–anther position and full blooming date in almond. A total of 275 SSR primer pairs selected from the previous studies of various Prunus species were tested in both populations. A total of 175 SSR loci segregated in 'Gulcan‐2 × Lauranne' population and 162 SSR loci were mapped into eight linkage groups. The total map length was 514.6 cM, with an average marker density of 3.2 cM. In 'Guara × Nurlu' population, 159 markers segregated, and 153 SSR loci were mapped. The total map length was 493.9 cM with an average marker distance of 3.2 cM. Five and four major QTLs were detected in 'Gulcan‐2 × Lauranne' and 'Guara × Nurlu' populations, respectively. The linkage maps constructed in this study can be used in QTL analysis of important phenotypic traits in almond, whereas identified QTL regions and closely related markers can be used for marker assisted selection in future almond breeding programmes. [ABSTRACT FROM AUTHOR]

In order to increase global wheat production, it is necessary to examine different ways of increasing yield. One of the solutions is to identify the genes that control different stress tolerance indices. This research aims to identify the genes controlling quantitative traits under normal conditions and salt stress in the germination stage. The experiments were carried out in a factorial form using a completely randomized design with 3 replications, on 107 lines resulted from the crossing of Gonbad and Zagros cultivars at Gonbad Kavous University, 2021. A linkage map was obtained using 519 SSR, 8 CAAT, 33 IJS, 47 iPBS, 3 IRAP, 17 RAPD, 8 SCoT and 12 ISSR markers on 21 wheat chromosomes. The length of the linkage map was 4918.94 cM and the distance between two adjacent markers about 5.55 cM. A total of 84 QTLs were detected in normal and salinity stress conditions (control, 6 dS/m, 12 dS/m), of which seven QTLs were related to control condition, 42 QTLs were related to 6 dS/m salinity stress and 35 QTLs were related to 12 dS/m stress condition. qLR-B3, qMGT-A5, qR/SDW-B2, qR/SDW-A3, qR/SDW-B7, qLS-A5 and qILVS-A5 were detected under control condition. qSLI-D6 was identified as a major QTL for SLI under 6 dS/m salinity stress by explaining more than 44% of the phenotypic variation of the trait. In the 12 dS/m salinity stress, several gene loci of large effect QTLs were detected, among which qIWVS-B3 explained more than 55% of the phenotypic diversity of the trait. After validation, the results of this research can introduce suitable candidates for marker-assisted selection programs in the population of Iranian wheat RILs. [ABSTRACT FROM AUTHOR]

Rice production relies on large amounts of synthetic nitrogen fertilizer to meet crop nutritional demands. However, the current fertilizer use efficiency is poor, with an average of 30–50% of total applied nitrogen (N) recovered in grains. Consequently, optimizing N availability and N use efficiency (NUE) has become a major target for rice yield improvement, and looking for quantitative trait loci (QTL) associated with NUE can provide useful information for developing nitrogen efficient rice genotypes. The present study aims to identify QTLs associated with NUE and its two components, agronomic NUE (agNUE) and grain nitrogen increase rate (GIR). A recombinant inbred line population (RIL) derived from a cross between Nipponbare and OM052, consisting of 159 F3 individuals was developed and cultivated in low-N (8 kg N/0.67 ha, N8) and high-N (18 kg N/0.67 ha, N18) conditions. Specific length amplified fragment sequencing (SLAF) was used to genotype the RILs and construct a high-density linkage map spanning 1587.70 cM, consisting 2707 SLAF markers with an average interval of 0.59 cM between adjacent marker loci. QTL analysis confirmed four significant QTLs distributed among chromosome 1, 6, and 11, with the proportion of phenotypic variance explained by each QTL ranging from 2.96 to 11.11% and LOD scores from 1.67 to 3.75. Functional annotation of genes located within the QTL intervals revealed NUE putative candidate genes. Overall, the QTLs identified in this study contribute information that could be useful for NUE improvement in rice. [ABSTRACT FROM AUTHOR]

Genomic analysis of hybrid zones offers unique insights into emerging reproductive isolation and the dynamics of introgression. Because hybrid genomes consist of blocks inherited from one or the other parental taxon, linkage information is essential. In most cases, the spectrum of local ancestry tracts can be efficiently uncovered from dense linkage maps. Here, we report the development of such a map for the hybridizing toads, Bombina bombina and Bombina variegata (Anura: Bombinatoridae). Faced with the challenge of a large (7-10Gb), repetitive genome, we set out to identify a large number of Mendelian markers in the nonrepetitive portion of the genome that report B. bombina vs B. variegata ancestry with appropriately quantified statistical support. Bait sequences for targeted enrichment were selected from a draft genome assembly, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Validation of the resulting map with 4755 markers underscored the large-scale synteny between Bombina and Xenopus tropicalis. By assessing the sex of late-stage F2 tadpoles from histological sections, we identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination. [ABSTRACT FROM AUTHOR]

Seed size is an important agronomic trait in watermelon, but the candidate genes and underlying molecular mechanism are not fully known. In the present study, genetic analysis of the BC1 population derived from two parental lines revealed that watermelon seed size is controlled by a single locus and medium seeds are dominant to tomato seeds. In addition, we constructed a genetic linkage map. The total length of the linkage map was 1629.92 cM, with an average distance of.16 cM. QTL mapping and resequencing analysis identified a 13.96‐kb chromosomal deletion on chromosome 2. There were only two genes (Cla97C02G045390 and Cla97C02G045400) present in the corresponding region. Transcriptome data of tomato seed and medium seed watermelons showed that the two genes were always highly expressed in medium seed plants but expressed at low or no levels in tomato seed plants. Moreover, two markers indicated that the genes were related to watermelon seed size. Our present study provides key genetic variation and potential candidate gene of watermelon seed size and lays the foundation for the molecular mechanism of seed size. [ABSTRACT FROM AUTHOR]

The stem color of young mung bean is a very useful tool in germplasm identification. Flowering time and plant height (PH) are known to be strongly correlated with crop adaption and yield. However, few studies have focused on elucidating the genetic mechanisms that regulate these five particular traits: young stem color (YSC), days to first flowering (DFF), days to maturity (DM), PH, and nodes on the main stem (NMS). In this study, a genetic linkage map for the F2 population was constructed using 129 InDel markers that were developed based on the sequence variations between parents. A total of 14 QTLs related to YSC, DFF, DM, PH, and NMS were detected. These QTLs were distributed on six chromosomes (1, 3, 4, 6, 7, and 10), which individually accounted for 1.32 to 90.07% of the total phenotypic variation. Using a short and high-density linkage map for the F3 population, six of the seven QTLs which clustered at two intervals on chromosomes 3 and 10 were detected again. Further analysis found that four QTLs between InDel markers R3-15 and R3-19 controlled DFF, DM, PH, and NMS, and each QTL accounted for a large percent of the total phenotypic variation. Analysis of two separated F2:3 lines also found that the phenotype was highly corresponded to its genotype which was between R3-15 and R3-19. Phenotype and genotype analysis for 30 mung bean accessions showed that the major effect QTL qDFF3 was a key regulator for DFF. Using a map-based cloning method, the major effect QTL qYSC4 for YSC was mapped in a 347 Kb interval on chromosome 4. Candidate gene analysis showed that sequence variations and expression level differences existed in the predicted candidate gene between the parents. These results provide a theoretical basis for cloning these QTLs and marker-assisted selection. [ABSTRACT FROM AUTHOR]

Background: Tambaqui (Colossoma macropomum, Cuvier, 1818) is the most economically important native freshwater fish species in Brazil. It can reach a total length of over 1 m and a weight of over 40 kg. The species displays a clear sex dimorphism in growth performance, with females reaching larger sizes at harvest. In aquaculture, the production of monosex populations in selective breeding programmes has been therefore identified as a key priority. Results: In the present study, a genetic linkage map was generated by double digest restriction-site associated DNA (ddRAD) sequencing from 248 individuals sampled from two F1 families. The map was constructed using 14,805 informative SNPs and spanned 27 linkage groups. From this, the tambaqui draft genome was improved, by ordering the scaffolds into chromosomes, and sex-linked markers were identified. A total of 235 markers on linkage group 26 showed a significant association with the phenotypic sex, supporting an XX/XY sex determination system in the species. The four most informative sex-linked markers were validated on another 206 sexed individuals, demonstrating an accuracy in predicting sex ranging from 90.0 to 96.7%. Conclusions: The genetic mapping and novel sex-linked DNA markers identified and validated offer new tools for rapid progeny sexing, thus supporting the development of monosex female production in the industry while also supporting breeding programmes of the species. [ABSTRACT FROM AUTHOR]

Marasmius oreades is a basidiomycete fungus that grows in so called "fairy rings," which are circular, underground mycelia common in lawns across temperate areas of the world. Fairy rings can be thought of as natural, long-term evolutionary experiments. As each ring has a common origin and expands radially outwards over many years, different sectors will independently accumulate mutations during growth. The genotype can be followed to the next generation, as mushrooms producing the sexual spores are formed seasonally at the edge of the ring. Here, we present new genomic data from 95 single-spore isolates of the species, which we used to construct a genetic linkage map and an updated version of the genome assembly. The 44-Mb assembly was anchored to 11 linkage groups, producing chromosome-length scaffolds. Gene annotation revealed 13,891 genes, 55% of which contained a pfam domain. The repetitive fraction of the genome was 22%, and dominated by retrotransposons and DNA elements of the KDZ and Plavaka groups. The level of assembly contiguity we present is so far rare in mushroom-forming fungi, and we expect studies of genomics, transposons, phylogenetics, and evolution to be facilitated by the data we present here of the iconic fairy-ring mushroom. [ABSTRACT FROM AUTHOR]

Background: Genomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.-A. cepa monosomic addition lines (MALs) and doubled haploids (DHs). These were the parental lines of an A. cepa mapping population for transcriptome-based SNP genotyping. Results: We mapped the transcriptome sequence reads from a series of A. fistulosum-A. cepa MALs onto the unigene sequence of the doubled haploid shallot A. cepa Aggregatum group (DHA) and compared the MAL genotype call for parental bunching onion and shallot transcriptome mapping data. We identified SNP sites with at least four reads on 25,462 unigenes. They were anchored on eight A. cepa chromosomes. A single SNP site was identified on 3,278 unigenes and multiple SNPs were identified on 22,184 unigenes. The chromosome marker information was made public via the web database Allium TDB (http://alliumtdb.kazusa.or.jp/). To apply transcriptome based genotyping approach for genetic mapping, we gathered RNA sequence data from 96 lines of a DHA × doubled haploid bulb onion A. cepa common onion group (DHC) mapping population. After selecting co-dominant SNP sites, 16,872 SNPs were identified in 5,339 unigenes. Of these, at least two SNPs with identical genotypes were found in 1,435 unigenes. We developed a linkage map using genotype information from these unigenes. All unigene markers mapped onto the eight chromosomes and graphical genotyping was conducted based on the unigene order information. Another 2,963 unigenes were allocated onto the eight chromosomes. To confirm the accuracy of this transcriptome-based genetic linkage map, conventional PCR-based markers were used for linkage analysis. All SNP - and PCR-based markers were mapped onto the expected linkage groups and no inconsistency was found among these chromosomal locations. Conclusions: Effective transcriptome analysis with unique Allium resources successfully associated numerous chromosome markers with unigene information and a high-density A. cepa linkage map. The information on these unigene markers is valuable in genome sequencing and useful trait detection in Allium. [ABSTRACT FROM AUTHOR]

Dry root rot (DRR) caused by Rhizoctonia bataticola [(Taub.) Butler] is an emerging disease of chickpea (Cicer arietinum L.) and a serious constraint to chickpea production in warm and arid regions. To identify the genomic regions conferring resistance to DRR, a total of 182 F9 derived Recombinant Inbred Lines (RILs) were developed from the cross between a susceptible line BG 212 and moderately resistant breeding line ICCV 08305. The parental lines and RILs were screened against Rb 6 isolate of R. bataticola using paper towel method under controlled environment at ICRISAT during 2016 and 2017. The RILs were genotyped with cost-effective SNP genotyping platform, Affymetrix® Axiom®CicerSNP array. As a result, a high-density genetic map with 13,110 SNP markers spanning 1224.11 cM with an average inter marker distance of 0.09 cM was developed. A single minor QTL ('qDRR-8') explaining 6.70% PVE with LOD scores 3.34 was identified on CaLG08 for DRR resistance which could be further explored for mining candidate genes and the linked SNP markers could be further validated for application in marker-assisted selection of DRR resistance in chickpea breeding programs. [ABSTRACT FROM AUTHOR]

The present study conducted QTL (quantitative trait locus) mapping using F2 and F2:3 generations derived from a cross between an overwintering cultivated rice Nuodao89-1 and Shuhui527, to identify potential yield component related QTLs. A total of 37 QTLs were detected across all chromosome except chromosome 7, with LOD values ranging from 3.10 to 12.67. Three QTLs including qTGW3.1, qTGW6.1 and qNEG9.1 were repeatedly detected in both generations. qTGW3.1 was from Nuodao89-1, a total of 46 functional genes involved in 229 gene ontology terms were identified within its locus. Six QTL clusters were founded and corresponding agronomic traits of those QTLs showed highly significant correlation. Three types of epistatic interaction including 47 epistatic QTL pairs for eight yield component traits were detected, but the epistatic QTLs was not so important in controlling the genetic expression of the yield-related Nuodao89-1 as the additive QTLs. Overall, this research provides a theoretical basis for the mining of yield-related genes from overwintering cultivated rice. [ABSTRACT FROM AUTHOR]

During the transition from sexual to asexual reproduction, a suite of reproduction‐related sexual traits become superfluous, and may be selected against if costly. Female functional virginity refers to asexual females resisting to mate or not fertilizing eggs after mating. These traits appear to be among the first that evolve during transitions from sexual to asexual reproduction. The genetic basis of female functional virginity remains elusive. Previously, we reported that female functional virginity segregates as expected for a single recessive locus in the asexual parasitoid wasp Asobara japonica. Here, we investigate the genetic basis of this trait by quantitative trait loci (QTL) mapping and candidate gene analyses. Consistent with the segregation of phenotypes, we found a single QTL of large effect, spanning over 4.23 Mb and comprising at least 131 protein‐coding genes, of which 15 featured sex‐biased expression in the related sexual species Asobara tabida. Two of the 15 sex‐biased genes were previously identified to differ between related sexual and asexual population/species: CD151 antigen and nuclear pore complex protein Nup50. A third gene, hormone receptor 4, is involved in steroid hormone mediated mating behaviour. Overall, our results are consistent with a single locus, or a cluster of closely linked loci, underlying rapid evolution of female functional virginity in the transition to asexuality. Once this variant, causing rejection to mate, has swept through a population, the flanking region does not get smaller owing to lack of recombination in asexuals. [ABSTRACT FROM AUTHOR]

The comma butterfly (Polygonia c-album , Nymphalidae, Lepidoptera) is a model insect species, most notably in the study of phenotypic plasticity and plant-insect coevolutionary interactions. In order to facilitate the integration of genomic tools with a diverse body of ecological and evolutionary research, we assembled the genome of a Swedish comma using 10X sequencing, scaffolding with matepair data, genome polishing, and assignment to linkage groups using a high-density linkage map. The resulting genome is 373 Mb in size, with a scaffold N50 of 11.7 Mb and contig N50 of 11,2Mb. The genome contained 90.1% of single-copy Lepidopteran orthologs in a BUSCO analysis of 5,286 genes. A total of 21,004 gene-models were annotated on the genome using RNA-Seq data from larval and adult tissue in combination with proteins from the Arthropoda database, resulting in a high-quality annotation for which functional annotations were generated. We further documented the quality of the chromosomal assembly via synteny assessment with Melitaea cinxia. The resulting annotated, chromosome-level genome will provide an important resource for investigating coevolutionary dynamics and comparative analyses in Lepidoptera. [ABSTRACT FROM AUTHOR]

• 17 SCAR markers linked to double flower trait of petunia hybrida was developed. • A high-density genetic map was constructed with 4474 SNP markers. • The double flower genes in petunia were first mapped to a genomic region of 1.82 Mb. Double flower (DF) is one of the important ornamental traits of horticultural plants, but the molecular mechanism of its formation is still unclear. In this study, forward genetic approaches were applied to explore the key genes involved in the DF formation in petunia. We developed a total of 17 SCAR markers linked to DF, and initially mapped the DF genes onto 9 scaffolds (totally 13.3 Mb) in the genome of the DF petunia. We also constructed a genetic linkage map of petunia, which contained 4474 SNP markers, with a total genetic distance of 2022.786 cM and an average genetic distance of 0.758 cM. In QTL analysis, a QTL associated with DF trait was detected. The LOD value of the marker was 3.82–12.71, and the contribution rate was 16.0 %–44.0 %. To further shorten the mapping interval of the DF genes, we constructed a near-isogenic line (NIL) population containing 2757 plants, and used these 17 SCAR markers to screen the recombinant plants, and located the DF genes within a 2.2 Mb interval. Combined with Bacterial Artificial Chromosome (BAC) library screening, the mapping interval of the DF genes was ultimately shortened from 2.2 Mb to 1.82 Mb. Presently, research on the DF trait of petunia mainly focused on the ABC(D)E model. The fine mapping results of petunia DF genes obtained in this study provide a new idea for revealing the molecular mechanism of DF formation in petunia. [ABSTRACT FROM AUTHOR]

Arctic and alpine, high latitude and high elevation environments are one of the most stressful environments for species to inhabit. This harshness manifests itself in lower species richness in comparison to more southern vegetation zones (Francis & Currie, 2003). Furthermore, the climatic oscillations—past and predicted—have the most dramatic effect on these ecosystems. For example, in regions of continental ice sheets—the northernmost part of Western Europe and North America—the Arctic species assemblages are no older than a few thousands of years, which is a relatively short period from an evolutionary perspective. Although similar environments may have existed further south during the Ice Age, allowing some preadaptation for the Arctic species, the current habitat is a unique combination of environmental factors such as the climate, soil, bedrock, and photoperiod. Hence, understanding the evolutionary forces shaping Arctic‐alpine species will be important for predicting these vulnerable environments' population viability and adaptive potential in the future. In this issue of Molecular Ecology Resources, Nowak et al. (Molecular Ecology Resources) present extensive genome‐wide resources for an Arctic‐alpine plant Draba nivalis. This adds a valuable new member into the cabbage family models for evolutionary genetics and adaptation studies, to accompany e.g., Arabidopsis (Nature Genetics, 43, 476; Nature, 408, 796), Arabis (Nature Plants, 1, 14023) and Capsella (Nature Genetics, 45, 831). A whole new avenue will open up for molecular ecological studies not only for D. nivalis, but the whole large Draba genus with its diverse ecological and evolutionary characteristics. [ABSTRACT FROM AUTHOR]

The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome‐scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short‐reads, single‐molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non‐Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation‐reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant. see also the Perspective by Tanja Pyhäjärvi and Tiina M. Mattila [ABSTRACT FROM AUTHOR]

Summary: A large F2 cross with 920 Japanese quail was used to map QTL for phosphorus utilization, calcium utilization, feed per gain and body weight gain. In addition, four bone ash traits were included, because it is known that they are genetically correlated with the focal trait of phosphorus utilization. Trait recording was done at the juvenile stage of the birds. The individuals were genotyped genome‐wide for about 4k SNPs and a linkage map constructed, which agreed well with the reference genome. QTL linkage mapping was performed using multimarker regression analysis in a line cross model. Single marker association mapping was done within the mapped QTL regions. The results revealed several genome‐wide significant QTL. For the focal trait phosphorus utilization, a QTL on chromosome CJA3 could be detected by linkage mapping, which was substantiated by the results of the SNP association mapping. Four candidate genes were identified for this QTL, which should be investigated in future functional studies. Some overlap of QTL regions for different traits was detected, which is in agreement with the corresponding genetic correlations. It seems that all traits investigated are polygenic in nature with some significant QTL and probably many other small‐effect QTL that were not detectable in this study. [ABSTRACT FROM AUTHOR]

On the basis of the genetic analysis of F2 by F3 in the combination M13 × r "e" + o, the recombination frequencies between genetic factors of chromosome 6 (=6H) barley were estimated. The study included the following genes: r "e"(smooth awns "e"), sex 1 (shrunken endosperm xenia 1), o (orange lemma 1), gs 4 (glossy sheath 4), and Amy 1–7 (α-amylase 1, type 7). The Amy 1 locus was identified by separation of alpha-amylase by electrophoresis at pH 8.3. On the basis of the five-point test, the following order to location of the studied loci in chromosome 6 (=6H) was established: 6S–r "e" (=raw 5)–gs 4 (=gsh 4)–o (=rob 1)–cen–Sex 1–Amy 1–6L. The linkage estimation and literature analysis showed that, among the indicated genes, the Amy 1 and Sex 1 loci are located in the long arm of chromosome 6. The other genetic factors are associated with the short arm of this chromosome. The centromere is between the genetic factors of Sex 1 and o (=rob 1). In general, the data presented indicate the need to review the genetic linkage map of chromosome 6 (=6H) barley. [ABSTRACT FROM AUTHOR]

A yellow inbred line (SP3B) and a red doubled haploid line (H6) were used to produce a F2 mapping population of onion (Allium cepa L.). Initially, insertion/deletion and cleaved amplified polymorphic sequence markers were developed based on polymorphisms in the reference transcriptome. To improve efficiency of marker development, RNA-seq was carried out to identify single nucleotide polymorphisms (SNPs) between parental lines. High-quality SNPs were selected via customized screening process, and 344 high resolution melting (HRM) markers were developed. In addition, 161 HRM markers were developed based on the SNPs detected using genotyping-by-sequencing. A linkage map consisting of 652 molecular markers distributed in eight linkage groups was constructed. The total length of the linkage map was 749.8 cM, and the average interval between markers was 1.91 cM, the highest resolution among onion linkage maps reported so far. All eight linkage groups were assigned to onion chromosomes by identifying the common homologous loci in other linkage maps. Four major loci (C, I, R, and L) determining onion bulb colors were located on separate chromosomes. Analysis of 'Santero', a F1 cultivar resistant to downy mildew, revealed that the length of the chromosome fragment introgressed from Allium roylei, harboring the resistance gene estimated at 27.6 cM at the end of chromosome 3. The high-resolution linkage map constructed in this study and chromosomal locations of major qualitative loci will be used to design an effective selection strategy for onion breeding programs. [ABSTRACT FROM AUTHOR]

Italian ryegrass (Lolium multiflorum Lam.) is widely cultivated in temperate regions owing to its excellent producibility and digestibility. Nitrogen is an essential nutrient for plant growth; however, the overuse of nitrogen fertilizers can lead to excessive accumulation of nitrate-nitrogen in Italian ryegrass, which can prove to be lethal for ruminants. To study the genetic control of the nitrate-nitrogen content in Italian ryegrass, an Italian ryegrass line LNG8 (with low 0.12% dry matter (DM) of nitrate-nitrogen) and a second line JFIR12 (with a "normal" 0.20% DM of nitrate-nitrogen) were pair-crossed and 190 F2 individuals derived from these were used to construct an SSR-based linkage map for conducting QTL analysis. A linkage map was constructed based on 212 Lolium SSR markers. The female parental map consisted of seven linkage groups (LGs) and had a total length of 714.1 cM with 178 loci and an average map density of 4.0 cM. The male parental map consisted of 7 LGs and had a total length of 737.4 cM with 199 loci and an average map density of 3.7 cM. We measured the nitrate-nitrogen content of the mapping population in three replicates (including the main stem and two tillers separated from the main stem) at the six-leaf stage. The nitrate-nitrogen content of the mapping population followed a normal distribution with a marginal skewness toward the lower parent. Our analysis revealed the presence of six QTLs on three LGs. A major QTL on LG1 was detected in all three replicates in both two-parental maps, which could explain 19.4%–29.9% of the phenotypic variation. Furthermore, based on the information of model plant species such as rice and Arabidopsis, we cloned six nitrogen metabolism-related genes and attempted to locate these on our linkage maps; however, none of these six genes were located in the demarcated QTL regions. These results will be useful for understanding the genetic bases of nitrate-nitrogen content in Italian ryegrass and the molecular cloning of QTLs for determination of nitrate-nitrogen content. The flanking markers of the QTLs will be helpful for breeding Italian ryegrass with low nitrate-nitrogen content. [ABSTRACT FROM AUTHOR]

Squamate reptiles exhibit high variation in their phenotypic traits and geographical distributions and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46-Gb genome assembly has a scaffold N50 of 11.52 Mb with N50 contig size of 220.4 kb and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total, 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles. [ABSTRACT FROM AUTHOR]

Genotyping-by-sequencing (GBS) allows rapid identification of markers for use in development of linkage maps, which expedite efficient breeding programs. In the present study, we have utilized GBS approach to identify and genotype single-nucleotide polymorphism (SNP) markers in an inter-specific RIL population of Cicer arietinum L. X C. reticulatum. A total of 141,639 raw SNPs were identified using the TASSEL-GBS pipeline. After stringent filtering, 8208 candidate SNPs were identified of which ~ 37% were localized in the intragenic regions followed by genic regions (~ 30%) and intergenic regions (~ 27%). We then utilized 6920 stringent selected SNPs from present study and 6714 SNPs and microsatellite markers available from previous studies for construction of linkage map. The resulting high-density linkage map comprising of eight linkage groups contained 13,590 markers which spanned 1299.14 cM of map length with an average marker density of 0.095 cM. Further, the derived linkage map was used to improve the available assembly of desi chickpea genome by anchoring 443 previously unplaced scaffolds onto eight linkage groups. The present efforts have refined anchoring of the desi chickpea genome assembly to 55.57% of the ~ 520 Mb of assembled desi genome. To the best of our knowledge, the linkage map generated in the present study represents one of the most dense linkage map developed for the crop till date. It will serve as a valuable resource for fine mapping and positional cloning of important quantitative trait loci (QTLs) associated with agronomical traits and also for anchoring and ordering of future genome sequence assemblies. [ABSTRACT FROM AUTHOR]