Codominant Markers Research Articles

A novel strategy to map a locus associated with flowering time in canola (Brassica napus L.).

Flowering time is an important agronomic trait for canola breeders, as it provides growers with options for minimizing exposure to heat stress during flowering and to more effectively utilize soil moisture. Plants have evolved various systems to control seasonal rhythms in reproductive phenology including an internal circadian clock that responds to environmental signals. In this study, we used canola cultivar 'Westar' as a recurrent parent and canola cultivar 'Surpass 400' as the donor parent to generate a chromosome segment substitution line (CSSL) and to map a flowering time locus on chromosome A10 using molecular marker-assisted selection. This CSSL contains an introgressed 4.6 mega-bases (Mb) segment (between 13 and 17.6Mb) of Surpass 400, which substantially delayed flowering compared with Westar. To map flowering time gene(s) within this locus, eight introgression lines (ILs) were developed carrying a series of different lengths of introgressed chromosome A10 segments using five co-dominant polymorphic markers located at 13.5, 14.0, 14.5, 15.0, 15.5, and 16.0Mb. Eight ILs were crossed with Westar reciprocally and flowering time of resultant 16 F1 hybrids and parents were evaluated in a greenhouse (2021 and 2022). Four ILs (IL005, IL017, IL035, and IL013) showed delayed flowering compared to Westar (P < 0.0001), and their reciprocal crosses displayed a phenotype intermediate in flowering time of both homozygote parents. These results indicated that flowering time is partial or incomplete dominance, and the flowering time locus mapped within a 1Mb region between two co-dominant polymorphic markers at 14.5-15.5Mb on chromosome A10. The flowering time locus was delineated to be between 14.60 and 15.5Mb based on genotypic data at the crossover site, and candidate genes within this region are associated with flowering time in canola and/or Arabidopsis. The co-dominant markers identified on chromosome A10 should be useful for marker assisted selection in breeding programs but will need to be validated to other breeding populations or germplasm accessions of canola.

Validation of molecular markers linked to bruchid resistance in green gram (&lt;i&gt;Vigna radiata&lt;/i&gt;)

The pulse beetle, Callosobruchus spp., poses a threat to legumes by consuming the protein content of the grain, resulting in potential losses in storage ranging from 12 to 30%. Molecular marker technology helps to mitigate the breeding constraint in the development of bruchid resistance in green gram breeding programmes. In the present study, validation of locus-specific STSbr1 and STSbr2 markers linked with bruchid resistance was done using fifteen genotypes viz., VBN (Gg) 2 (susceptible) and Vigna radiata var. sublobata/2 (resistant), F1 hybrid, two susceptible and ten resistant RILs derived from the above parents. The marker STS br1 behaved as a dominant marker and produced an approximate allele size of 225 bp in the resistant parent, F1 hybrid and resistant RILs and absent in susceptible parent and susceptible RILs, which showed cent per cent co-segregation with bruchid resistance locus. Hence, it is concluded that STS br1 is linked with bruchid-resistant genes. The marker STS br2 behaved as a co-dominant marker and produced an approximate allele size of 470 bp in all the 15 genotypes evaluated (monomorphic) and did not differentiate the resistant and susceptible genotypes. The marker STS br1 could be used in marker-assisted selection to develop bruchid-resistant varieties and to screen the germplasm to identify bruchid-resistant donors in green gram.

Identification of molecular markers linked to leaf rust resistance gene Lr13 in wheat

Aim. Identification of codominant molecular markers closely linked to the Lr13 leaf rust resistance gene. Methods. PCR with detection in a polyacrylamide gel. Hybridological analysis. Phytopathology evaluation. Statistical analysis. Results. PCR analysis of varieties carrying the Lr13 gene and near-isogenic lines of the Thatcher variety with genes for resistance to leaf rust Lr13 (TcLr13), Lr16 (TcLr16), Lr23 (TcLr23) and the F2 population TcLr13 x TcLr34 by the microsatellite loci Xbarc13, Xbarc55, Xgwm148, Xwmc261, Xgwm271, Xwmc272, Xwmc344, Xbarc361, Xgwm410, Xwmc474, Xwmc477 and Xgwm630 was performed. To test the two microsatellite loci Xgwm148 and Xwmc344 as candidate markers for the Lr13 gene, we used the F2 population, which was obtained from crossing two near-isogenic lines of the Thatcher variety with leaf rust resistance genes Lr13 (TcLr13) and Lr34 (TcLr34). Conclusions. When comparing the genotyping data of F2 hybrids and the phenotypic manifestation of resistance to leaf rust, it was determined that the microsatellite locus Xwmc344 is closely linked to the Lr13 gene.

Development of a Greenhouse Assay to Screen Soybean Varieties for Resistance to Aerial Blight Caused by Rhizoctonia solani Anastomosis Group 1-IA.

Aerial blight, caused by the fungus Rhizoctonia solani anastomosis group (AG) 1-IA, is an economically important soybean disease in the mid-Southern United States. Management has relied on fungicide applications during the season, but there is an increasing prevalence of resistance to commonly used strobilurin fungicides and an urgent need to identify soybean varieties resistant to aerial blight. Because the patchy distribution of the pathogen complicates field variety screening, the present study aimed to develop a greenhouse screening protocol to identify soybean varieties resistant to aerial blight. For this, 88 pathogen isolates were collected from commercial fields and research farms across five Louisiana parishes, and 77% were confirmed to be R. solani AG1-IA. Three polymorphic codominant microsatellite markers were used to explore the genetic diversity of 43 R. solani AG1-IA isolates, which showed high genetic diversity, with 35 haplotypes in total and only two haplotypes common to two other locations. Six genetically diverse isolates were chosen and characterized for their virulence and fungicide sensitivity. The isolate AC2 was identified as the most virulent and was resistant to both active ingredients, azoxystrobin and pyraclostrobin, tested. The six isolates were used in greenhouse variety screening trials using a millet inoculation protocol. Of the 31 varieties screened, only Armor 48-D25 was classified as moderately resistant, and plant height to the first node influenced final disease severity. The study provides short-term solutions for growers to choose less susceptible varieties for planting and lays the foundation to characterize host resistance against this important soybean pathogen.

TriticeaeSSRdb: a comprehensive database of simple sequence repeats in Triticeae.

Microsatellites, known as simple sequence repeats (SSRs), are short tandem repeats of 1 to 6 nucleotide motifs found in all genomes, particularly eukaryotes. They are widely used as co-dominant markers in genetic analyses and molecular breeding. Triticeae, a tribe of grasses, includes major cereal crops such as bread wheat, barley, and rye, as well as abundant forage and lawn grasses, playing a crucial role in global food production and agriculture. To enhance genetic work and expedite the improvement of Triticeae crops, we have developed TriticeaeSSRdb, an integrated and user-friendly database. It contains 3,891,705 SSRs from 21 species and offers browsing options based on genomic regions, chromosomes, motif types, and repeat motif sequences. Advanced search functions allow personalized searches based on chromosome location and length of SSR. Users can also explore the genes associated with SSRs, design customized primer pairs for PCR validation, and utilize practical tools for whole-genome browsing, sequence alignment, and in silico SSR prediction from local sequences. We continually update TriticeaeSSRdb with additional species and practical utilities. We anticipate that this database will greatly facilitate trait genetic analyses and enhance molecular breeding strategies for Triticeae crops. Researchers can freely access the database at http://triticeaessrdb.com/.

Identification of candidate genes for adult plant stripe rust resistance transferred from Aegilops ventricosa 2NvS into wheat via fine mapping and transcriptome analysis.

An adult plant gene for resistance to stripe rust was narrowed down to the proximal one-third of the 2NvS segment translocated from Aegilops ventricosa to wheat chromosome arm 2AS, and based on the gene expression analysis, two candidate genes were identified showing a stronger response at the adult plant stage compared to the seedling stage. The 2NvS translocation from Aegilops ventricosa, known for its resistance to various diseases, has been pivotal in global wheat breeding for more than three decades. Here, we identified an adult plant resistance (APR) gene in the 2NvS segment in wheat line K13-868. Through fine mapping in a segregating near-isogenic line (NIL) derived population of 6389 plants, the candidate region for the APR gene was narrowed down to between 19.36Mb and 33Mb in the Jagger reference genome. Transcriptome analysis in NILs strongly suggested that this APR gene conferred resistance to stripe rust by triggering plant innate immune responses. Based on the gene expression analysis, two disease resistance-associated genes within the candidate region, TraesJAG2A03G00588940 and TraesJAG2A03G00590140, exhibited a stronger response to Puccinia striiformis f. sp. tritici (Pst) infection at the adult plant stage than at the seedling stage, indicating that they could be potential candidates for the resistance gene. Additionally, we developed a co-dominant InDel marker, InDel_31.05, for detecting this APR gene. Applying this marker showed that over one-half of the wheat varieties approved in 2021 and 2022 in Sichuan province, China, carry this gene. Agronomic trait evaluation of NILs indicated that the 2NvS segment effectively mitigated the negative effects of stripe rust on yield without affecting other important agronomic traits. This study provided valuable insights for cloning and breeding through the utilization of the APR gene present in the 2NvS segment.

Identification of allelic relationship and translocation region among chromosomal translocation lines that leads to less-seed watermelon.

Less-seed and seedless traits are desirable characteristics in watermelon (Citrullus lanatus). Hybridization between watermelon chromosomal translocated lines and wild lines significantly reduced seed counts in the hybrid fruits, approaching even seedless. However, the allelic relationships and the chromosomal translocation breakpoints from different sources are unclear, which limits their utility in breeding practices. This study focused on three groups of chromosomal translocation materials from different sources and conducted inheritance and allelic relationship analysis of translocation points. The results from third-generation genome sequencing and fluorescence in situ hybridization (FISH) revealed that the specific translocations in the naturally mutated material MT-a involved reciprocal translocations between Chr6 and Chr10. The Co60γ radiation-induced mutant material MT-b involved reciprocal translocations between Chr1 and Chr5, Chr4 and Chr8. The Co60γ radiation-induced mutant material MT-c involved complex translocations among Chr1, Chr5, and Chr11. Cytological observation showed that heterozygous translocation hybrids showed chromosomal synapsis abnormalities during meiotic diakinesis. Further, dominant and codominant molecular markers were developed on both sides of the translocation breakpoints, which could facilitate rapid and efficient identification of chromosome translocation lines. This study provides technical guidance for utilizing chromosomal translocation materials in the development of less-seed watermelon varieties.

Investigation of Imidazolinone Herbicide Resistance Gene with KASP Markers for Japonica/Geng Rice Varieties in the Huanghuaihai Region of China.

Rice is a staple food for more than half of the global population due to its food security and sustainable development. Weeds compete with crops for sunlight and indispensable nutrients, affecting the yield and quality of crops. Breeding herbicide-tolerant rice varieties paired with herbicide application is expected to help with weed control. In this study, 194 Japonica/Geng rice varieties or lines collected from the Huanghuaihai region of China were screened by Kompetitive Allele-Specific PCR (KASP) markers based on four mutation sites within OsALS1 (LOC_Os02g30630), which is the target of imidazolinone (IMI) herbicides. Only the OsALS1627N haplotype was identified in 18 varieties, including the previously reported Jingeng818 (JG818), and its herbicide resistance was validated by treatment with three IMIs. To investigate the origin of the OsALS1627N haplotype in the identified varieties, six codominant PCR-based markers tightly linked with OsALS1 were developed. PCR analysis revealed that the other 17 IMI-tolerant varieties were derived from JG818. We randomly selected three IMI-tolerant varieties for comparative whole-genome resequencing with known receptor parent varieties. Sequence alignment revealed that more loci from JG818 have been introduced into IMI-tolerant varieties. However, all three IMI-tolerant varieties carried clustered third type single nucleotide polymorphism (SNP) sites from unknown parents, indicating that these varieties were not directly derived from JG818, whereas those from different intermediate improved lines were crossed with JG818. Overall, we found that only OsALS1627N from JG818 has been broadly introduced into the Huanghuaihai region of China. Additionally, the 17 identified IMI-tolerant varieties provide alternative opportunities for improving such varieties along with other good traits.

Perangkat Lunak Perhitungan Hereditas Pada Tumbuhan

Deadlock Metode codominant marker data is often carried out with the assumption that the marker is dominant, an approach that can oversimplify results and lead to erroneous conclusions. The aim of this paper is to provide a practical guide to conducting codominant data analysis and selecting appropriate software. We provide an overview of the computational methods and basic principles required for statistical analysis of codominant molecular markers to evaluate genetic diversity and molecular characterization of germplasm collections. Each software package is evaluated by analyzing the same set of data. Differences between parameters are detailed, and comments are provided regarding the software output. This paper aims to provide a better understanding of the differences among available software packages, so that researchers can make a choice that suits their codominant genetic analysis needs. spoken in English.

Development and application of a codominant marker of the melon rind colour gene CmAPRR2

AbstractRind colour is an important quality attribute of melon appearance. Identifying target genes and developing functional molecular markers is significant for rind colour breeding in melon. This study involved a genetic analysis of the fruit rind colours of two inbred lines: H185 (with black green melon rind) and H160 (with white rind) alongside a fruit rind colour gene, CmAPRR2. The purpose was to discover the variation sites of the CmAPRR2 gene and develop specific molecular marker for rind colour in melon. The results showed that the black green rind is dominant over white, and single gene controls the colours. A mutation of the G856T base occurred in the eighth exon of the CmAPRR2 coding DNA region in H160, suggesting that this mutation is the key factor for the white rind colour. Thus, a codominant molecular marker, FC, for gene CmAPRR2 was developed and used for molecular identification of 189 F2 individuals. The marker revealed a complete correspondence between genotype and phenotype. Additionally, the marker revealed that the other four white rinds had G856T mutations. This study provides a basis for targeted improvement of melon rind colours, offering a technical means for molecular marker‐assisted breeding of melon rind colours.

Detection Of Sm Gene Resistance To Gray Leaf Spot In (Stemphylium Spp.) Tomato Cultivars Iraq

Abstract Gray leaf spot, Occurs due to Stemphylium spp., is a foliar disease in tomato. The Resistance against gray leaf spot disease is conferred by a single incompletely dominant gene Sm located on chromosome 11. This study aimed to identify cultivar resistant alleles or susceptible alleles by molecular marker tightly linked to the Sm gene and the use of marker-assisted selection inbreeding. In this study, we used eight tomato cultivars Farmed in Iraq. The analysis demonstrated that the co-dominant marker Sm-InDel, which produced 122-bp fragment for resistance in seven genotypes and a 140-bp fragment for susceptible alleles in one genotype, respectively could be utilized in Marker-assisted selection (MAS)for gray leaf spot resistance.

Cross-Species Transferability of Specific SSR Markers from Carex curvula (Cyperaceae) to Other Carex Species

Microsatellites are codominant markers that, due to their high polymorphism, are a common choice for detecting genetic variability in various organisms, including fungi, plants, and animals. However, the process of developing these markers is both costly and time-consuming. As a result, the cross-species amplification has become a more rapid and more affordable alternative in biological studies. The objective of this study was to assess the applicability of 13 SSR markers, originally designed for Carex curvula, in other 14 species belonging to different sections of the genus. All the markers were successfully transferred with a mean of 90.76%, and 100% transferability was reached in two species (C. baldensis and C. rupestris). The lowest transferability was registered in the G165 marker, which did not produce amplification in six species. Together, the microsatellites amplified a total of 183 alleles, ranging from 10 to 19 alleles per locus, with an average of 14.07. The mean number of different alleles ranged from 0.846 to a maximum of 2.077 per locus. No significant departures from the Hardy–Weinberg equilibrium were detected in polymorphic loci. The transferability of the 13 SSR markers proved highly successful in various Carex species, across different clades and sections of the genus.

ОЦЕНКА АЛЛЕЛЬНОГО СОСТОЯНИЯ ГЕНА FAOMT У СЕЛЕКЦИОННЫХ ФОРМ ЗЕМЛЯНИКИ МЕЖСОРТОВОГО ПРОИСХОЖДЕНИЯ

Improving the fruit aroma is one of the promising directions of modern strawberry breeding. The strawberry fruit aroma is a complex trait, formed by a combination of a large number of volatile compounds. The present study shows the results of assessing the allelic state of the FaOMT gene, determining biosynthesis of mesifurane (volatile compound) in strawberry selected forms created in the «I.V. Michurin FSC». The biological objects of the study were 22 strawberry selected intervarietal forms from 12 crossing combinations. The allelic state of the FaOMT gene was identified using codominant SCAR marker FaOMT-SI/NO. As a result of the studies, the marker fragment of the functional allele FaOMT+ was identified in 86.4 % of forms. A heterozygous combination of alleles of the FaOMT gene (average level of mesifurane accumulation in fruits) was detected in 9.1 % forms. The homozygous state of the functional allele was detected in 77.3% forms. The homozygous state of the non-functional allele FaOMT- (mesifurane is not produced) is characterized by three genotypes (13.6 %). The greatest value for strawberry breeding use are forms with the homozygous state of the FaOMT+ allele: 1/6-41 (Vima Zanta × Polka), 2/2-32, 2/2-41 (Faith × Tea), 3/2-62 (Vima Zanta × Privlekatelnaya), 3/4-6, 3/4-7 (Malwina × Tea), 3/9-5, 3/9-12 (Florence × Faith), 5/1-105 (Polka × Vima Zanta), 5/2-23, 5/2-26, 5/2-32 (San Andreas × Monterey), 6/3-5, 6/3-21 (Kimberly × 9/2-2), 7/2-78 (Asia × Maya), 9/2-2, 9/2-7 (Kimberly × Honeoye). These forms are characterized by the maximum level of mesifurane biosynthesis in fruits and their involvement of which in hybridization allows the transmission of the target allele to 100 % of the hybrid seedlings.

Genetic analysis of invasive spread of wintercreeper (Euonymus fortunei), a popular ornamental groundcover

AbstractAn important route of introduction of some nonnative species that subsequently become invasive in the United States is through horticulture. One such plant is Euonymus fortunei (Turcz.) Hand.-Maz., commonly known as wintercreeper, an evergreen groundcover with more than 52 different horticultural varieties, which is still sold at many plant nurseries and garden centers in the midwestern United States. Although several states have recognized E. fortunei as an invasive species, it is unknown how its escape from cultivation has occurred and even the identity of spreading populations, including whether hybrids or cultivars are involved. Using codominant microsatellite markers, we sampled multiple invasive populations in Ohio, Kentucky, Kansas, and Minnesota and compared their genotypes with commercially available cultivars to determine how spread has occurred. All samples collected from invasive populations were genetically identical to one another and matched perfectly with the ‘Coloratus’ cultivar, the only cultivar to exhibit polyploidy. The data also suggest that E. fortunei may potentially reproduce via apomixis and/or clonally through propagule fragments, which can quickly fix favorable genotypes within a population. To curb continued invasive spread, we suggest that Coloratus be removed from commercial sale and distribution. We also propose that land managers, horticultural and landscaping businesses, and governmental agencies carefully monitor other Euonymus cultivars for invasive potential and spread.

Efficiency of RAPD and SSR markers in assessing genetic diversity in summer onion (Allium cepa L.) genotypes

The genetic diversity assessment of agricultural crops is crucial for breeding programs aimed at enhancing crop yield, resistance to diseases, and adaptation to changing environmental conditions. In the present investigation, a comparative genetic relationship in sixteen onion genotypes was assessed utilizing dominant (RAPD) and co-dominant (SSR) marker systems. Ten RAPD and nine SSR markers showed genetic diversity remarkably and produced 503 and 107 amplicons respectively. Spearman rank correlation was used to compare the different efficiency parameters in two marker systems with respect to sixteen onion genotypes. The genetic relationship based on similarity matrix values between a pair of cultivars was higher for SSR markers than for the RAPD marker system. OPC-04 (RAPD primer) and ACM-004 (SSR primer) witnessed the highest poly-morphic bands along with other polymorphic markers that proved to be useful in grouping onion genotypes. Finally, dendrograms were constructed and compared following the mantel test to find out the genetic diversity among the germplasms. This study will be effective for a selection of efficient primers and suitable marker systems to distinguish the onion genotypes in the future.

Registration of eight germplasm lines of upland cotton (Gossypium hirsutum L.) resistant to reniform nematodes (Rotylenchulus reniformis) with elite agronomic performance

AbstractCotton (Gossypium hirsutum L.) germplasm lines BARBREN‐713‐8 (Reg. no. GP‐1138, PI 701080), BARBREN‐713‐11 (Reg. no. GP‐1131, PI 701073), BARBREN‐713‐13 (Reg. no. GP‐1132, PI 701074), BARBREN‐713‐25 (Reg. no. GP‐1133, PI 701075), BARBREN‐713‐32 (Reg. no. GP‐1134, PI 701076), BARBREN‐713‐33 (Reg. no. GP‐1135, PI 701077), BARBREN‐713‐41 (Reg. no. GP‐1136, PI 701078), and BARBREN‐713‐48 (Reg. no. GP‐1137, PI 701079) were developed and released by the USDA‐ARS, Texas A&amp;M AgriLife Research, and Cotton Incorporated in 2014. The objective of the release was to provide breeders with agronomically elite germplasm that is resistant to reniform nematode (Rotylenchulus reniformis). Four lines (BARBREN‐713‐8, ‐32, ‐33, and ‐48) also have simple sequence repeat (SSR) DNA markers for the Mi‐1 or Mi‐2 gene for resistance to root‐knot nematode [Meloidogyne incognita (Kolfoid &amp; White) Chitwood]. The lines have excellent seedling vigor in fields infested with both nematodes and fungal root‐rot pathogens. Resistance to reniform nematode was transferred from G. barbadense GB713 (PI 608139) and is associated primarily with the Ren2GB713 gene on chromosome 21. This gene could be detected with the codominant SSR marker BNL3279_105 or the single nucleotide polymorphism marker GI‐187401. In controlled environment assays, these lines reported here suppressed numbers of reniform nematode eggs by 74–92% compared with ‘FiberMax FM966’. The lines outyielded and had fiber quality equal to or greater than several commercial cultivars.

Applicability of a new sex-linked codominant DNA marker among asparagus cultivars and various Asparagus species

Applicability of a new sex-linked codominant DNA marker among asparagus cultivars and various <i>Asparagus</i> species

Genomics-assisted genetics of complex regions from chickpea chromosome 4 reveals two candidate genes for Ascochyta blight resistance

Ascochyta blight (AB) disease caused by the fungus Ascochyta rabiei is a major threat to global chickpea production. Molecular breeding for improved AB resistance requires the identification of robust fine-mapped QTLs/candidate genes and associated markers. Earlier, we identified three QTLs (qABR4.1, qABR4.2, and qABR4.3) for AB resistance on chickpea chromosome 4 by employing multiple quantitative trait loci sequencing strategy on an intra-specific (FLIP84–92C x PI359075) and an inter-specific (FLIP84–92C x PI599072) crosses derived recombinant inbred lines. Here, we report the identification of AB resistance providing candidate genes under the fine mapped qABR4.2 and qABR4.3 genomic region by combining genetic mapping, haplotype block inheritance, and expression analysis. The qABR4.2 region was narrowed down from 5.94 Mb to ∼800 kb. Among 34 predicted gene models, a secreted class III peroxidase encoding gene showed higher expression in AB-resistant parent after A. rabiei conidia inoculation. Under qABR4.3, we identified a frame-shift mutation in a cyclic nucleotide-gated channel CaCNGC1 gene leading to the truncated N-terminal domain in resistant accession of chickpea. The extended N-terminal domain of CaCNGC1 interacts with chickpea calmodulin. Thus, our analysis has revealed narrowed genomic regions and their associated polymorphic markers, namely CaNIP43 and CaCNGCPD1. These co-dominant markers significantly associate with AB resistance on qABR4.2 and qABR4.3 regions. Our genetic analysis revealed that the presence of AB-resistant alleles at two major QTLs (qABR4.1 and qABR4.2) together provide AB resistance in the field while minor QTL qABR4.3 determines the degree of resistance. The identified candidate genes and their diagnostic markers will assist in the biotechnological advancement and introgression of AB resistance into locally adapted chickpea varieties used by farmers.

Seedless fruit in Annona squamosa L. is monogenic and conferred by INO locus deletion in multiple accessions

Key messageInheritance of the presence/absence of seeds in Annona squamosa is mediated by a single fully recessive gene and is caused by a deletion of the INNER NO OUTER (INO) locus.For some fruits, seedless varieties are desirable for consumption and processing. In the sugar apple tree (Annona squamosa L.), the seedless trait in the Thai seedless (Ts) and Brazilian seedless (Bs) accessions was associated with defective ovules and an apparent deletion of the INNER NO OUTER (INO) ovule development gene locus. Segregation analysis of F2 and backcross descendants of crosses of Bs to fertile wild-type varieties in this species with a multi-year generation time showed that seedlessness was recessive and controlled by a single locus. Comparison of whole genome sequence of a wild-type plant and a third accession, Hawaiian seedless (Hs), identified a 16 kilobase deletion including INO in this line. Ts and Bs lines were shown to have an identical deletion, indicating a common origin from a single deletion event. Analysis of microsatellite markers could not preclude the possibility that all three seedless accessions are vegetatively propagated clones. The sequence of the deletion site enabled a codominant assay for the wild-type and mutant genes allowing observation of complete cosegregation of the seedless/defective ovule phenotype with the INO deletion, showing maximal separation of less than 3.5 cM. The observed deletion is the only significant difference between the wild-type and Hs line over 587 kilobases, likely encompassing much more than 3.5 cM, showing that the deletion is the cause of seedless trait. The codominant markers and obtained progenies will be useful for introgression of the seedless trait into elite sugar apple lines and into other Annonas through interspecific crossings.

Identification of sex-linked codominant markers and development of a rapid LAMP-based genetic sex identification method in channel catfish (Ictalurus punctatus)

Channel catfish (Ictalurus punctatus), a commercially important aquaculture species, is native to North America and has spread worldwide. Channel catfish exhibit sexual size dimorphism, with males growing faster than females. Therefore, the creation of an all-male population is promising for growth improvement in channel catfish. In the process of monosex fish breeding, the development of sex-specific genetic markers is the most critical step. Although sex-linked SSRs and SNPs have been developed in channel catfish, they are polymorphic, unstable, and difficult to use for rapid sex genotyping. In this study, three codominant markers with large size differences between their two alleles were identified by performing a detailed comparison of the region on X and Y chromosomes that enriched male-specific SNPs using preexisting RAD-seq data and genome data. After examination by one wild and three artificially bred populations using electrophoresis on agarose gel, the accuracy rate reached 100%, suggesting that all three codominant markers could be effectively used for genetic sex identification in channel catfish. To achieve genetic sex identification performed in the field without complex equipment, a rapid LAMP-based method was established for the identification of genetic sex in channel catfish based on the codominant markers we identified. Overall, this study established rapid and effective PCR- and LAMP-based methods to identify the genetic sex of channel catfish in the laboratory and in the field.