Fine-mapping of a major QTL controlling plant height by BSA-seq and transcriptome sequencing in cotton.

KEY MESSAGE: GhSOT (GH_D05G3950) plays a negative role in regulating plant height development by modulating the GA signaling. Plant height is an important indicator affecting mechanical harvesting for cotton. Therefore, understanding the genes associated with the plant height is crucial for cotton breeding and production. In this study, we used bulk segregant analysis sequencing to identify a new quantitative trait locu (QTL) called qPH5.1, which is linked to plant height. Local QTL mapping using seven kompetitive allele-specific PCR (KASP) markers and linkage analysis successfully narrowed down qPH5.1 to ~ 0.34 Mb region harbored five candidate genes. Subsequently, RNA sequencing (RNA-seq) analysis and examination of expression patterns revealed that GhSOT exhibited the highest likelihood of being the candidate gene responsible for the plant height at this locus. Seven SNP site variations were identified in the GhSOT promoter between the two parents, and Luciferase experiments confirmed that the promoter of GhSOT from cz3 enhances downstream gene expression more effectively. Additionally, suppression of GhSOT in cz3 resulted in the restoration of plant height, further emphasizing the functional significance of this gene. Application of exogenous gibberellin acid (GA) significantly restored plant height in cz3, as demonstrated by RNA-seq analysis and exogenous hormone treatment, which revealed alterations in genes associated with GA signaling pathways. These results reveal GhSOT is a key gene controlling plant height, which may affect plant height by regulating GA signaling.

QTL analysis of native Fusarium head blight and deoxynivalenol resistance in 'D8006W'/'Superior', soft white winter wheat population.

BACKGROUND: Fusarium head blight (FHB), caused by Fusarium graminearum, is a major disease of wheat in North America. FHB infection causes fusarium damaged kernels (FDKs), accumulation of deoxynivalenol (DON) in the grain, and a reduction in quality and grain yield. Inheritance of FHB resistance is complex and involves multiple genes. The objective of this research was to identify QTL associated with native FHB and DON resistance in a 'D8006W'/'Superior', soft white winter wheat population. RESULTS: Phenotyping was conducted in replicated FHB field disease nurseries across multiple environments and included assessments of morphological and FHB related traits. Parental lines had moderate FHB resistance, however, the population showed transgressive segregation. A 1913.2 cM linkage map for the population was developed with SNP markers from the wheat 90 K Infinium iSelect SNP array. QTL analysis detected major FHB resistance QTL on chromosomes 2D, 4B, 5A, and 7A across multiple environments, with resistance from both parents. Trait specific unique QTL were detected on chromosomes 1A (visual traits), 5D (FDK), 6B (FDK and DON), and 7D (DON). The plant height and days to anthesis QTL on chromosome 2D coincided with Ppd-D1 and were linked with FHB traits. The plant height QTL on chromosome 4B was also linked with FHB traits; however, the Rht-B1 locus did not segregate in the population. CONCLUSIONS: This study identified several QTL, including on chromosome 2D linked with Ppd-D1, for FHB resistance in a native winter wheat germplasm.

Quantitative trait loci analysis for molecular markers linked to agricultural traits of Pleurotus ostreatus.

Pleurotus ostreatus is a global mushroom crop with nutritional and medicinal benefits. However, the genetic basis of several commercial traits remains unknown. To address this, we analyzed the quantitative trait loci (QTLs) for two representative cultivars, "Heuktari" and "Miso," with apparently distinct alleles. A genetic map with 11 linkage groups was constructed, in which 27 QTLs were assigned to 14 traits. The explained phenotypic variations in QTLs ranged from 7.8% to 22.0%. Relatively high LOD values of 6.190 and 5.485 were estimated for the pinheading period and the number of valid stipes, respectively. Some QTL-derived molecular markers showed potential enhancement rates of selection precision in inbred lines, especially for cap shape (50%) and cap thickness (30%). Candidate genes were inferred from the QTL regions and validated using qRT-PCR, particularly for the cysteine and glutathione pathway, in relation to cap yellowness. The molecular markers in this study are expected to facilitate the breeding of the Heuktari and Miso lines and provide probes to identify related genes in P. ostreatus.

Deciphering the genetic basis of agronomic, yield, and nutritional traits in rice (Oryza sativa L.) using a saturated GBS-based SNP linkage map.

Developing high-yielding rice varieties that possess favorable agronomic characteristics and enhanced grain Zn content is crucial in ensuring food security and addressing nutritional needs. This research employed ICIM, IM, and multi-parent population QTL mapping methods to identify important genetic regions associated with traits such as DF, PH, NT, NP, PL, YLD, TGW, GL, GW, Zn, and Fe. Two populations of recombinant inbred lines consisting of 373 lines were phenotyped for agronomic, yield and grain micronutrient traits for three seasons at IRRI, and genotyped by sequencing. Most of the traits demonstrated moderate to high broad-sense heritability. There was a positive relationship between Zn and Fe contents. The principal components and correlation results revealed a significant negative association between YLD and Zn/Fe. ICIM identified 81 QTLs, while IM detected 36 QTLs across populations. The multi-parent population analysis detected 27 QTLs with six of them consistently detected across seasons. We shortlisted eight candidate genes associated with yield QTLs, 19 genes with QTLs for agronomic traits, and 26 genes with Zn and Fe QTLs. Notable candidate genes included CL4 and d35 for YLD, dh1 for DF, OsIRX10, HDT702, sd1 for PH, OsD27 for NP, whereas WFP and OsIPI1 were associated with PL, OsRSR1 and OsMTP1 were associated to TGW. The OsNAS1, OsRZFP34, OsHMP5, OsMTP7, OsC3H33, and OsHMA1 were associated with Fe and Zn QTLs. We identified promising RILs with acceptable yield potential and high grain Zn content from each population. The major effect QTLs, genes and high Zn RILs identified in our study are useful for efficient Zn biofortification of rice.

Fine Mapping and Candidate Gene Analysis of Two Major Quantitative Trait Loci, qFW2.1 and qFW3.1, Controlling Fruit Weight in Pepper (Capsicum annuum).

Fruit weight is an important agronomic trait in pepper production and is closely related to yield. At present, many quantitative trait loci (QTL) related to fruit weight have been found in pepper; however, the genes affecting fruit weight remain unknown. We analyzed the fruit weight-related quantitative traits in an intraspecific Capsicum annuum cross between the cultivated species blocky-type pepper, cv. Qiemen, and the bird pepper accession, "129-1" (Capsicum annuum var. glatriusculum), which was the wild progenitor of C. annuum. Using the QTL-seq combined with the linkage-based QTL mapping approach, QTL detection was performed; and two major effects of QTL related to fruit weight, qFW2.1 and qFW3.1, were identified on chromosomes 2 and 3. The qFW2.1 maximum explained 12.28% of the phenotypic variance observed in two F2 generations, with the maximum LOD value of 11.02, respectively; meanwhile, the qFW3.1 maximum explained 15.50% of the observed phenotypic variance in the two F2 generations, with the maximum LOD value of 11.36, respectively. qFW2.1 was narrowed down to the 1.22 Mb region using homozygous recombinant screening from BC2S2 and BC2S3 populations, while qFW3.1 was narrowed down to the 4.61Mb region. According to the transcriptome results, a total of 47 and 86 differentially expressed genes (DEGs) in the candidate regions of qFW2.1 and qFW3.1 were identified. Further, 19 genes were selected for a qRT-PCR analysis based on sequence difference combined with the gene annotation. Finally, Capana02g002938 and Capana02g003021 are the most likely candidate genes for qFW2.1, and Capana03g000903 may be a candidate gene for qFW3.1. Taken together, our results identified and fine-mapped two major QTL for fruit weight in pepper that will facilitate marker-assistant breeding for the manipulation of yield in pepper.

High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing.

Camellia oleifera, an important tree species and source of edible oil in China, has received significant attention owing to the oil's high unsaturated fatty acid content, which has benefits for human health. However, the mechanisms underlying C. oleifera yield and oil quality are largely unknown. In this study, 180 F1 progenies were obtained from two parents with obvious differences in fruit- and oil-related traits. We constructed a high-density genetic map using a double digest restriction site-associated DNA sequencing (ddRAD-Seq) strategy in C. oleifera. This map spanned 3327 cM and anchored 2780 markers in 15 linkage groups (LGs), with an average marker interval of 1.20 cM. A total of 221 quantitative trait loci (QTLs) associated with fruit- and oil-related traits were identified across three years' worth of phenotypic data. Nine QTLs were detected simultaneously in at least two different years, located on LG02, LG04, LG05, LG06, and LG11, and explained 8.5-16.6% of the phenotypic variation in the corresponding traits, respectively. Seventeen major QTLs were obtained that explained 13.0-16.6% of the phenotypic variance. Eleven and five flanking SNPs of major QTLs for fruit- and oil-related traits were detected which could be used for marker-assisted selection in C. oleifera breeding programs. Furthermore, 202 potential candidate genes in QTL regions were identified based on the collinearity of the genetic map and the C. oleifera "CON" genome. A potential regulatory network controlling fruit development and oil biosynthesis was constructed to dissect the complex mechanism of oil accumulation. The dissection of these QTLs will facilitate the gene cloning underlying lipid synthesis and increase our understanding in order to enhance C. oleifera oil yield and quality.

Fine mapping of stem rust resistance derived from soft red winter wheat cultivar AGS2000 to an NLR gene cluster on chromosome 6D.

The Puccinia graminis f. sp. tritici (Pgt) Ug99-emerging virulent races present a major challenge to global wheat production. To meet present and future needs, new sources of resistance must be found. Identification of markers that allow tracking of resistance genes is needed for deployment strategies to combat highly virulent pathogen races. Field evaluation of a DH population located a QTL for stem rust (Sr) resistance, QSr.nc-6D from the breeding line MD01W28-08-11 to the distal region of chromosome arm 6DS where Sr resistance genes Sr42, SrCad, and SrTmp have been identified. A locus for seedling resistance to Pgt race TTKSK was identified in a DH population and an RIL population derived from the cross AGS2000 × LA95135. The resistant cultivar AGS2000 is in the pedigree of MD01W28-08-11 and our results suggest that it is the source of Sr resistance in this breeding line. We exploited published markers and exome capture data to enrich marker density in a 10 Mb region flanking QSr.nc-6D. Our fine mapping in heterozygous inbred families identified three markers co-segregating with resistance and delimited QSr.nc-6D to a 1.3 Mb region. We further exploited information from other genome assemblies and identified collinear regions of 6DS harboring clusters of NLR genes. Evaluation of KASP assays corresponding to our co-segregating SNP suggests that they can be used to track this Sr resistance in breeding programs. However, our results also underscore the challenges posed in identifying genes underlying resistance in such complex regions in the absence of genome sequence from the resistant genotypes.

Identification of stripe rust resistance gene YrBDT in Chinese landrace wheat Baidatou using BSE-seq and BSR-seq.

KEY MESSAGE: A new stripe rust resistance gene YrBDT in Chinese landrace wheat Baidatou was mapped to a 943.6-kb interval on chromosome arm 6DS and co-segregated with a marker CAPS3 developed from candidate gene TraesCS6D03G0027300. Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a devastating foliar disease of wheat. Chinese landrace wheat Baidatou has shown high resistance to a broad spectrum of Pst races at both the seedling and adult-plant stages for decades in the Longnan region of Gansu province, a hot spot for stripe rust epidemics. Here, we report fine mapping and candidate gene analysis of stripe rust resistance gene YrBDT in Baidatou. Analysis of F1, F2 plants and F2:3 lines indicated that resistance in Baidatou to Pst race CYR31 was conferred by a single dominant gene, temporarily designated YrBDT. Bulked segregant exome capture sequencing (BSE-seq) analysis revealed 61 high-confidence polymorphic SNPs concentrated in a 5.4-Mb interval at the distal of chromosome arm 6DS. Several SNPs and InDels were also identified by genome mining of DNA sampled from the parents and contrasting bulks. The YrBDT locus was mapped to a 943.6-kb (4,658,322-5,601,880 bp) genomic region spanned by markers STS2 and STS3 based on IWGSC RefSeq v2.1, including five putative disease resistance genes. There was high collinearity of the target interval among Chinese Spring RefSeq v2.1, Ae. tauschii AL8/78 and Fielder genomes. The expression level of TraesCS6D03G0027300 showed significant association with Pst infection, and a gene-specific marker CAPS3 developed from TraesCS6D03G0027300 co-segregated with YrBDT suggesting this gene as a candidate of YrBDT. The resistance gene and flanking markers can be used in marker-assisted selection for improvement of stripe rust resistance.

Exploration and genetic analyses of canopy leaf pigmentation changes in soybean (Glycine max L.): unveiling a novel phenotype.

KEY MESSAGE: Pigmentation changes in canopy leaves were first reported, and subsequent genetic analyses identified a major QTL associated with levels of pigmentation changes, suggesting Glyma.06G202300 as a candidate gene. An unexpected reddish-purple pigmentation in upper canopy leaves was discovered during the late reproductive stages in soybean (Glycine max L.) genotypes. Two sensitive genotypes, 'Uram' and PI 96983, exhibited anomalous canopy leaf pigmentation changes (CLPC), while 'Daepung' did not. The objectives of this study were to: (i) characterize the physiological features of pigmented canopy leaves compared with non-pigmented leaves, (ii) evaluate phenotypic variation in a combined recombinant inbred line (RIL) population (N = 169 RILs) under field conditions, and (iii) genetically identify quantitative trait loci (QTL) for CLPC via joint population linkage analysis. Comparison between pigmented and normal leaves revealed different Fv/Fm of photosystem II, hyperspectral reflectance, and cellular properties, suggesting the pigmentation changes occur in response to an undefined abiotic stress. A highly significant QTL was identified on chromosome 6, explaining ~ 62.8% of phenotypic variance. Based on the QTL result, Glyma.06G202300 encoding flavonoid 3'-hydroxylase (F3'H) was identified as a candidate gene. In both Uram and PI 96983, a 1-bp deletion was confirmed in the third exon of Glyma.06G202300 that results in a premature stop codon in both Uram and PI 96983 and a truncated F3'H protein lacking important domains. Additionally, gene expression analyses uncovered significant differences between pigmented and non-pigmented leaves. This is the first report of a novel symptom and an associated major QTL. These results will provide soybean geneticists and breeders with valuable knowledge regarding physiological changes that may affect soybean production. Further studies are required to elucidate the causal environmental stress and the underlying molecular mechanisms.

Whole Genome Analysis in Consanguineous Families Reveals New Loci for Speech Sound Disorder (SSD).

Speech is the most common means of communication in humans. Any defect in accurate speech production ability results in the development of speech sound disorder (SSD), a condition that can significantly impair an individual's academic performance, social interactions, and relationships with peers and adults. This study investigated the genetic basis of SSD in three Pakistani families. We performed family-based genome-wide parametric linkage analysis and homozygosity mapping in three consanguineous families with SSD from the Punjab province of Pakistan. The Test for Assessment of Articulation and Phonology in Urdu (TAAPU) was used to analyze the speech articulation data and determine the Percentage Correct Consonants (PCC) score. The PCC score defined the affected and unaffected individuals in each family. Parametric linkage analysis revealed a linkage to chromosome 5 (5q21.3-5q23.1) with a significant logarithm of the odds (LOD) score of 3.13 in a Pakistani family with specific language impairment-97 (PKSLI-97) under an autosomal recessive mode of inheritance. The other two families showed a suggestive linkage at 6p22.1, 14q12, and 16q12.1 under the recessive mode of inheritance. Interestingly, homozygosity mapping showed a loss of heterozygosity in the linkage region at 5q15-5q23.1, shared among seven affected (mostly in the younger generation) and one unaffected individual of PKSLI-97. Our analysis identified the 6p22 locus previously implicated in dyslexia, childhood apraxia of speech (CAS), and language impairment, confirming the role of KIAA0319 and DCDC2 in this locus. These findings provide statistical evidence for the genomic regions associated with articulation disorder and offer future opportunities to further the role of genes in speech production.

Cytogenetic identification and molecular mapping for the wheat-Thinopyrum ponticum introgression line with resistance to Fusarium head blight.

KEY MESSAGE: Xinong 511, a new wheat-Thinopyrum ponticum variety with excellent fusarium head blight resistance, the QTLs were mapped to the wheat chromosomes 5B and 7A with named QFhb.nwafu-5B and QFhb.nwafu-7A, respectively. Novel Fusarium head blight (FHB) resistance germplasms and genes are valuable for wheat improvement and breeding efforts. Thinopyrum ponticum, a wild relative of common wheat, is a valuable germplasm of disease resistance for wheat improvement and breeding. Xinong 511 (XN511) is a high-quality wheat variety widely cultivated in the Yellow and Huai Rivers Valley of China with stable FHB-resistance. Through analysis of pedigree materials of the wheat cultivar XN511, we found that the genetic material and FHB resistance from Th. ponticum were transmitted to the introgression line, indicating that the FHB resistance in XN511 likely originates from Th. ponticum. To further explore the genetic basis of FHB resistance in XN511, QTL mapping was conducted using the RILs population of XN511 and the susceptible line Aikang 58 (AK58). Survey with makers closely-linked to Fhb1, Fhb2, Fhb4, Fhb5, and Fhb7, indicated that both XN511 and the susceptible lines do not contain these QTL. Using bulked segregant analysis RNA-seq (BSR-Seq) and newly developed allele-specific PCR (AS-PCR) markers, QTLs in XN511 were successfully located on wheat chromosomes 5B and 7A. These findings are significant for further understanding and utilizing FHB resistance genes in wheat improvement.

Identification of QTLs associated with yield-related traits and superior genotype prediction using recombinant inbred line population in tobacco.

Tobacco is an economically significant industrial crop and model plant for genetic research, yet little is known about its genetic architecture. Quantitative trait loci (QTL) analysis was performed for six agronomic traits on an F_7 population of 341 genotypes, parents, and F1 plants using 1974 SSR markers across two environments. 31 QTLs contributing single-locus additive effects on 13 linkage groups (LGs) and 6 QTL pairs contributing epistatic effects on 6 LGs, were detected by the QTLNetwork 2.0 which was developed for the mixed-linear-model-based composite interval mapping (MCIM). Notably, 5 QTLs and 1 epistatic QTL pair were found to have pleiotropic effects on some genetically related traits. Moreover, the Broad sense heritability of the detected QTLs ranged from 1.05% to 43.33%, while genotype-by-environment interaction heritability spanned from 27.09% to 56.25%. Based on the results of QTL mapping, the potential superior lines for all or specific environments were designed and evaluated. Five major QTLs were finely dissected based on the tobacco reference genome of K326, and 31 candidate genes were predicted. This study offered new insights into the complicated genetic architecture and QTL resources for efficient breeding design for genetic improvement of agronomic traits in tobacco.

Selection with two alleles of X-linkage and its application to the fitness component analysis of OdsH in Drosophila.

In organisms with the XY sex-determination system, there is an imbalance in the inheritance and transmission of the X chromosome between males and females. Unlike an autosomal allele, an X-linked recessive allele in a female will have phenotypic effects on its male counterpart. Thus, genes located on the X chromosome are of particular interest to researchers in molecular evolution and genetics. Here we present a model for selection with two alleles of X-linkage to understand fitness components associated with genes on the X chromosome. We apply this model to the fitness analysis of an X-linked gene, OdsH (16D), in the fruit fly Drosophila melanogaster. The function of OdsH is involved in sperm production and the gene is rapidly evolving under positive selection. Using site-directed gene targeting, we generated functional and defective OdsH variants tagged with the eye-color marker gene white. We compare the allele frequency changes of the two OdsH variants, each directly competing against a wild-type OdsH allele in concurrent but separate experimental populations. After 20 generations, the two genetically modified OdsH variants displayed a 40% difference in allele frequencies, with the functional OdsH variant demonstrating an advantage over the defective variant. Using maximum likelihood estimation, we determined the fitness components associated with the OdsH alleles in males and females. Our analysis revealed functional aspects of the fitness determinants associated with OdsH, and that sex-specific fertility and viability consequences both contribute to selection on an X-linked gene.

Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies.

Admixture between populations and species is common in nature. Since the influx of new genetic material might be either facilitated or hindered by selection, variation in mixture proportions along the genome is expected in organisms undergoing recombination. Various graph-based models have been developed to better understand these evolutionary dynamics of population splits and mixtures. However, current models assume a single mixture rate for the entire genome and do not explicitly account for linkage. Here, we introduce TreeSwirl, a novel method for inferring branch lengths and locus-specific mixture proportions by using genome-wide allele frequency data, assuming that the admixture graph is known or has been inferred. TreeSwirl builds upon TreeMix that uses Gaussian processes to estimate the presence of gene flow between diverged populations. However, in contrast to TreeMix, our model infers locus-specific mixture proportions employing a hidden Markov model that accounts for linkage. Through simulated data, we demonstrate that TreeSwirl can accurately estimate locus-specific mixture proportions and handle complex demographic scenarios. It also outperforms related D- and f-statistics in terms of accuracy and sensitivity to detect introgressed loci.

A catalogue of recombination coldspots in interspecific tomato hybrids.

Increasing natural resistance and resilience in plants is key for ensuring food security within a changing climate. Breeders improve these traits by crossing cultivars with their wild relatives and introgressing specific alleles through meiotic recombination. However, some genomic regions are devoid of recombination especially in crosses between divergent genomes, limiting the combinations of desirable alleles. Here, we used pooled-pollen sequencing to build a map of recombinant and non-recombinant regions between tomato and five wild relatives commonly used for introgressive tomato breeding. We detected hybrid-specific recombination coldspots that underscore the role of structural variations in modifying recombination patterns and maintaining genetic linkage in interspecific crosses. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. About two-thirds of the genome are conserved coldspots, located mostly in the pericentromeres and enriched with retrotransposons. The coldspots also harbor genes associated with agronomic traits and stress resistance, revealing undesired consequences of linkage drag and possible barriers to breeding. We presented examples of linkage drag that can potentially be resolved by pairing tomato with other wild species. Overall, this catalogue will help breeders better understand crossover localization and make informed decisions on generating new tomato varieties.

Consensus genetic linkage map and QTL mapping allow to capture the genomic regions associated with agronomic traits in pearl millet.

MAIN CONCLUSION: A genetic linkage map representing the pearl millet genome was constructed with SNP markers. Major and stable QTL associated with flowering, number of productive tillers, ear head length, and test weight were mapped on chromosomes 1 and 3. Pearl millet (Pennisetum glaucum) is a major cereal and fodder crop in arid and semi-arid regions of Asia and Africa. Agronomic traits are important traits in pearl millet breeding and genetic and environmental factors highly influence them. In the present study, an F9 recombinant inbred line (RIL) population derived from a cross between PT6029 and PT6129 was evaluated for agronomic traits in three environments. Utilizing a genotyping by sequencing approach, a dense genetic map with 993 single nucleotide polymorphism markers covering a total genetic distance of 1035.4 cM was constructed. The average interval between the markers was 1.04 cM, and the seven chromosomes varied from 115.39 to 206.72 cM. Quantitative trait loci (QTL) mapping revealed 35 QTL for seven agronomic traits, and they were distributed on all pearl millet chromosomes. These QTL individually explained 11.35 to 26.71% of the phenotypic variation, with LOD values ranging from 2.74 to 5.80. Notably, four QTL (qDFF1.1, qNPT3.1, qEHL3.1, and qTW1.1) associated with days to fifty percent flowering, the number of productive tillers, ear head length, and test weight were found to be major and stable QTL located on chromosomes 1 and 3. Collectively, our results provide an important base for understanding the genetic architecture of agronomic traits in pearl millet, which is useful for accelerating the genetic gain toward crop improvement.

One-factor sex determination evolves without linkage between feminizing and masculinizing mutations.

The evolution of separate sexes from cosexuality requires at least two mutations: a feminizing allele to cause female development and a masculinizing allele to cause male development. Classically, the double mutant is assumed to be sterile, which leads to two-factor sex determination where male and female sex chromosomes differ at two loci. However, several species appear to have one-factor sex determination where sexual development depends on variation at a single locus. We show that one-factor sex determination evolves when the double mutant develops as a male or a female. The feminizing allele fixes when the double mutant is male, and the masculinizing allele fixes when the double mutant is female. The other locus then gives XY or ZW sex determination based on dominance: for example, a dominant masculinizer becomes a Y chromosome. Although the resulting sex determination system differs, the conditions required for feminizers and masculinizers to spread are the same as in classical models, with the important difference that the two alleles do not need to be linked. Thus, we reveal alternative pathways for the evolution of sex determination and discuss how they can be distinguished using new data on the genetics of sex determination.

Genetic Analysis of an F2 Population Derived from the Cotton Landrace Hopi Identified Novel Loci for Boll Glanding.

Landraces are an important reservoir of genetic variation that can expand the narrow genetic base of cultivated cotton. In this study, quantitative trait loci (QTL) analysis was conducted using an F2 population developed from crosses between the landrace Hopi and inbred TM-1. A high-density genetic map spanning 2253.11 and 1932.21 cM for the A and D sub-genomes, respectively, with an average marker interval of 1.14 cM, was generated using the CottonSNP63K array. The linkage map showed a strong co-linearity with the physical map of cotton. A total of 21 QTLs were identified, controlling plant height (1), bract type (1), boll number (1), stem color (2), boll pitting (2), fuzz fiber development (2), boll shape (3), boll point (4), and boll glanding (5). In silico analysis of the novel QTLs for boll glanding identified a total of 13 candidate genes. Analysis of tissue-specific expression of the candidate genes suggests roles for the transcription factors bHLH1, MYB2, and ZF1 in gland formation. Comparative sequencing of open reading frames identified early stop codons in all three transcription factors in Hopi. Functional validation of these genes offers avenues to reduce glanding and, consequently, lower gossypol levels in cottonseeds without compromising the defense mechanisms of the plant against biotic stresses.

Improved assembly of the Pungitius pungitius reference genome.

The nine-spined stickleback (Pungitius pungitius) has been increasingly used as a model system in studies of local adaptation and sex chromosome evolution but its current reference genome assembly is far from perfect, lacking distinct sex chromosomes. We generated an improved assembly of the nine-spined stickleback reference genome (98.3% BUSCO completeness) with the aid of linked-read mapping. While the new assembly (v8) was of similar size as the earlier version (v7), we were able to assign 4.4 times more contigs to the linkage groups and improve the contiguity of the genome. Moreover, the new assembly contains a ∼22.8 Mb Y-linked scaffold (LG22) consisting mainly of previously assigned X-contigs, putative Y-contigs, putative centromere contigs, and highly repetitive elements. The male individual showed an even mapping depth on LG12 (pseudo X chromosome) and LG22 (Y-linked scaffold) in the segregating sites, suggesting near-pure X and Y representation in the v8 assembly. A total of 26,803 genes were annotated, and about 33% of the assembly was found to consist of repetitive elements. The high proportion of repetitive elements in LG22 (53.10%) suggests it can be difficult to assemble the complete sequence of the species' Y chromosome. Nevertheless, the new assembly is a significant improvement over the previous version and should provide a valuable resource for genomic studies of stickleback fishes.

Identification of anther thermotolerance genes by the integration of linkage and association analysis in maize.

Maize is one of the world's most important staple crops, yet its production is increasingly threatened by the rising frequency of high-temperature stress (HTS). To investigate the genetic basis of anther thermotolerance under field conditions, we performed linkage and association analysis to identify HTS response quantitative trait loci (QTL) using three recombinant inbred line (RIL) populations and an association panel containing 375 diverse maize inbred lines. These analyses resulted in the identification of 16 co-located large QTL intervals. Among the 37 candidate genes identified in these QTL intervals, five have rice or Arabidopsis homologs known to influence pollen and filament development. Notably, one of the candidate genes, ZmDUP707, has been subject to selection pressure during breeding. Its expression is suppressed by HTS, leading to pollen abortion and barren seeds. We also identified several additional candidate genes potentially underly QTL previously reported by other researchers. Taken together, our results provide a pool of valuable candidate genes that could be employed by future breeding programs aiming at enhancing maize HTS tolerance.