F3 Families Research Articles

Construction of first genetic linkage map based on microsatellite markers and characterization of di- and tri-nucleotide microsatellite markers for Crassostrea hongkongesis

Hong Kong oyster Crassostrea hongkongensis is an important aquaculture species in the coastal areas of southern China. Because of its high demand and reasonable price, the production of Cohnella hongkongensis has increased drastically. However, the aquaculture of C. hongkongensis has also encountered some problems, such as seasonal mass mortality and reduction of availability and quality of wild seeds. Genetic linkage map is an effective tool for analyzing economically important traits. In this study, a consensus genetic map of C. hongkongensis was constructed by using microsatellite markers of F1 family. The consensus linkage map contained 104 loci, with a span of 653.9 cM and an average resolution of 6.9 cM. The estimated coverage of consensus linkage map was 85%. We identified 10 linkage groups, which were consistent with the haploid chromosome number of the species. The linkage map of male C. hongkongensis comprised 57 markers with a span of 467.6 cM, while the linkage map of female C. hongkongensis comprised 72 markers with a span of 570.9 cM. The average recombination ratio between males and females was 1:1.2. This map is vital for future QTL mapping framework of C. hongkongensis to perform marker assisted selection. Moreover, compared with di-nucleotide microsatellite markers, tri-nucleotide microsatellite markers have significantly stronger correlation with functional genes and cross-amplification success. We also found that the application potential of tri-nucleotide microsatellite markers in molecular-marker assisted selection gene mapping, and comparative linkage mapping was greater than that of di-nucleotide markers.

Identification of superior transgressive segregants in F2 and F3 populations of wheat (Triticum aestivum L.) for yield and its contributing traits

An experiment was carried out in timely sown condition during Rabi, 2018-20 to study the genetic variability, correlation, heritability and expected genetic advance for 13 traits in F2 and F3 populations of two wheat crosses and consequently identify superior transgressive segregants. The experimental material consisted of an F2 population of two crosses K 0307 × LOK 1 (cross 1) and HD 2733 × HUW 234 (cross 2) evaluated in an unreplicated trial and seeds of each identified transgressive segregants in F2 generation was forwarded to F3 generation for its evaluation and further sorting the superior segregants to be carry forwarded. The identified transgressive segregants exhibited a wide range of variation for all the traits except for spike length, indicating the presence of enough genetic variability in the material under study. The phenotypic coefficients of variation (PCV) values were higher than genotypic coefficients of variation (GCV) values for most of the traits studied. Estimates of genetic parameters, PCV and GCV in K 0307 × LOK 1 was highest for spikelets per spike and lowest for days to 50% flowering and days to maturity in both F2 and F3. While, highest for yield per plant and lowest for days to 50% flowering and days to maturity in HD 2733 × HUW 234. High heritability coupled with high genetic advance was recorded for spikelets per spike, test weight in a cross 1, in both F2 and F3. Similarly in cross 2, high heritability coupled with high genetic advance was recorded for grain filling days and yield per plant. Correlation analysis suggested that yield had a positive and significant relationship with test weight, grain per spike, and spikelets per spike for the F3 families of transgressive segregants of the cross 1. In cross 2, test weight, grain per spike, number of effective tillers, spikelets per spike, peduncle length, days to 50% flowering, and plant height had a positive and significant relationship with yield. Keywords: F2, F3 PCV, GCV, Heritability, Genetic advance, Transgressive segregants.

Strategies of preserving genetic diversity while maximizing genetic response from implementing genomic selection in pulse breeding programs

Key messageGenomic selection maximizes genetic gain by recycling parents to germplasm pool earlier and preserves genetic diversity by restricting the number of fixed alleles and the relationship in pulse breeding programs.Using a stochastic computer simulation, we investigated the benefit of optimization strategies in the context of genomic selection (GS) for pulse breeding programs. We simulated GS for moderately complex to highly complex traits such as disease resistance, grain weight and grain yield in multiple environments with a high level of genotype-by-environment interaction for grain yield. GS led to higher genetic gain per unit of time and higher genetic diversity loss than phenotypic selection by shortening the breeding cycle time. The genetic gain obtained from selecting the segregating parents early in the breeding cycle (at F1 or F2 stages) was substantially higher than selecting at later stages even though prediction accuracy was moderate. Increasing the number of F1 intercross (F1i) families and keeping the total number of progeny of F1i families constant, we observed a decrease in genetic gain and increase in genetic diversity, whereas increasing the number of progeny per F1i family while keeping a constant number of F1i families increased the rate of genetic gain and had higher genetic diversity loss per unit of time. Adding 50 F2 family phenotypes to the training population increased the accuracy of genomic breeding values (GEBVs) and genetic gain per year and decreased the rate of genetic diversity loss. Genetic diversity could be preserved by applying a strategy that restricted both the percentage of alleles fixed and the average relationship of the group of selected parents to preserve long-term genetic improvement in the pulse breeding program.

Genomic compatibility and inheritance of hexaploid-derived Fusarium head blight resistance genes in durum wheat.

Hexaploid-derived resistance genes exhibit complex inheritance and expression patterns in tetraploid backgrounds. This study aimed to characterize the inheritance patterns and genomic compatibilities of hexaploid-derived Fusarium head blight (FHB) resistance genes in tetraploid durum wheat (Triticum durumDesf.). Evaluation of FHB resistance for F1 hybrids of hexaploid 'Sumai 3' crossed with tetraploid and hexaploid wheats indicated that Sumai 3-derived FHB resistance genes exhibit a dominant phenotypic effect seen only in hexaploid hybrids. Alternately, the hexaploid-derived FHB resistance genes from PI 277012 exhibited complete dominance in the crosses with both tetraploid and hexaploid wheat. FHB evaluation of the F1 hybrids of Sumai 3 and PI 277012 crossed with 'Langdon' (LDN)-'Chinese Spring' D-genome substitution lines suggested that chromosomes 2B, 3B, 4B, 5B, 6B, 3A, 4A, 6A, and 7A contain genes that suppress expression of the Sumai 3-derived FHB resistance, whereas chromosomes 4A, 6A, and 6B contain genes required for expression of PI 277012-derived FHB resistance. A wide range of segregation for FHB severity (10-90%) was observed in the F2 generation of Sumai 3 crossed with durum cultivars LDN and 'Divide', but the distribution of F3 families derived from the most resistant F2 segregants was skewed towards susceptibility. Similar segregation trends were observed in the crosses of PI 277012 with other durum wheats, whereby FHB resistance became slightly diluted over successive generations. These results suggest tetraploid durum wheat contains the unique alleles at multiple gene loci on different chromosomes that positively and/or negatively regulate the expression of hexaploid-derived FHB resistance genes, which complicate efforts to deploy these genes in durum breeding programs.

A high-density genetic linkage map and QTL mapping for growth related traits in grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella), one of the most important freshwater food fish, has made a great contribution to freshwater aquaculture in China. Though a consensus linkage map of grass carp has been reported, the low marker resolution limited its application in fine mapping quantitative trait loci (QTL) of commercially important traits. In this study, a high-density linkage map was constructed based on a full-sib F1 family of grass carp, which was further used for mapping QTL for five growth related traits: body weight (BWE), body length (BL), body width (BWI), body height (BH) and fatness (FN). This high-density genetic map was constructed with 3979 SNPs, consisting of 24 linkage groups (LGs). The total length of the linkage map was 1752.742 cM, with an average marker resolution of 0.44 cM. QTL mapping analysis detected two significant and 19 suggestive QTL for the five morphometric traits, distributed on 8 LGs. The phenotypic variations explained of these QTL ranged from 7.2% to 32.8%. Finally, comparative genomic analysis revealed that 23 out of the 24 LGs of grass carp showed high synteny with 23 chromosomes of zebrafish. Taken together, the high-density linkage map and the 21 growth-related QTL, provide valuable genomic resources for both marker-assisted selection (MAS) and comparative genomic studies in grass carp and its related species.

Identification and Characterisation of Stripe Rust Resistance Genes Yr66 and Yr67 in Wheat Cultivar VL Gehun 892

Wheat cultivar VL Gehun 892 has shown a high level of resistance against Australian Puccinia striiformis f. sp. tritici (Pst) pathotypes. In this study, it was crossed with Westonia, a susceptible wheat cultivar, and digenic segregation was observed in the derived population against Pst pathotype 134 E16A+Yr17+Yr27+. Single-gene recombinant inbred line (RIL) populations were developed from F3 families (VL Gehun 892/Westonia#1 and VLGehun 892/Westonia#4) that showed monogenic segregations with two distinct phenotypes. Single-gene segregation against Pst pathotype 134 E16A+Yr17+Yr27+ was confirmed in both F6 RIL populations. Bulked segregant analysis using a 90K Infinium SNP array placed YrVL1 in the short arm of chromosome 3D and YrVL2 in the long arm of chromosome 7B. Kompetitive allele specific polymerase chain reaction (KASP) assays were developed for the SNPs linked with YrVL1 and YrVL2 and were mapped onto the respective populations. KASP_48179 (0.6 cM proximal) and KASP_18087 (2.1 cM distal) flanked YrVL1, whereas YrVL2 was mapped between KASP_37096 (1.2 cM proximal) and KASP_2239 (3.6 cM distal). Based on their pathotypic specificities, map locations, and stages of expression, YrVL1 and YrVL2 were demonstrated to be unique loci and named Yr66 and Yr67, respectively. Markers linked with these genes showed more than 85% polymorphism when tested on a set of 89 Australian cultivars and hence could be used for the marker-assisted selection of these genes in wheat breeding programs, following checks of parental polymorphisms.

Construction of Genetic Linkage Maps From a Hybrid Family of Large Yellow Croaker (Larimichthys crocea).

Consensus and sex-specific genetic linkage maps for large yellow croaker (Larimichthys crocea) were constructed using samples from an F1 family produced by crossing a Daiqu female and a Mindong male. A total of 20,147 single nucleotide polymorphisms (SNPs) by restriction site associated DNA sequencing were assigned to 24 linkage groups (LGs). The total length of the consensus map was 1757.4 centimorgan (cM) with an average marker interval of 0.09 cM. The total length of female and male linkage map was 1533.1 cM and 1279.2 cM, respectively. The average female-to-male map length ratio was 1.2 ± 0.23. Collapsed markers in the genetic maps were re-ordered according to their relative positions in the ASM435267v1 genome assembly to produce integrated genetic linkage maps with 9885 SNPs distributed across the 24 LGs. The recombination pattern of most LGs showed sigmoidal patterns of recombination, with higher recombination in the middle and suppressed recombination at both ends, which corresponds with the presence of sub-telocentric and acrocentric chromosomes in the species. The average recombination rate in the integrated female and male maps was respectively 3.55 cM/Mb and 3.05 cM/Mb. In most LGs, higher recombination rates were found in the integrated female map, compared to the male map, except in LG12, LG16, LG21, LG22, and LG24. Recombination rate profiles within each LG differed between the male and the female, with distinct regions indicating potential recombination hotspots. Separate quantitative trait loci (QTL) and association analyses for growth related traits in 6 months fish were performed, however, no significant QTL was detected. The study indicates that there may be genetic differences between the two strains, which may have implications for the application of DNA-information in the further breeding schemes.

Analysis of Yield Components on Seed Yield in F4 Families of Rice (Oryza sativa L.)

The experiment was conducted in a population comprising 30 F4 families of rice (Oryza sativa L.) derived from 15 different crosses. The effects of 10 yield components viz., plant height, panicle length, flag leaf area, panicle number, number of primary and secondary branches panicle-1, spikelet number panicle-1, spikelet ferilty per cent, 100-grain weight, grain yield panicle-1 on grain yield plant-1 were studied. Association studies indicated that correlations of grain yield with primary branches panicle-1, secondary branches panicle-1, number of spikelet and grain yield panicle-1 were positive and significant at both genotypic and phenotypic levels. Path analyses at both genotypic and phenotypic revealed that the direct selection for primary branches panicle-1 and secondary branches panicle-1 with restricted selection for number of panicles, length for panicle and 100-grain weight will increase the yield of rice in the population under study comprising F4 families of rice.

Could the Dilatata group of Paspalum be bred as sexual species? A preliminary assessment

AbstractPaspalum dilatatum Poir. is a perennial apomictic and pentaploid South American grass and a very valued forage crop. The species has been available commercially in several parts of the world; however, its low seed production, apomictic reproduction and ergot susceptibility are important limitations for its adoption and breeding. The Dilatata complex includes five sexual tetraploid mostly selfing species, very closely related to P. dilatatum, which can be hybridized in different combinations. To explore the productive potential of breeding this species group as a sexual selfing tetraploid by combining germplasm from different tetraploid sources, a cross was made between Paspalum flavescens and Paspalum plurinerve which showed high productivity and resistance to ergot. The F1 was compared to the parents and 20 F3 families to evaluate the presence of heterosis, and estimate the additive genetic variance and the degree of transgressive segregation for morphological and productive traits. The F1 showed heterosis for dry matter and the number of fertile tillers, while the F3 showed transgressive segregation in more than 30% of the families for most traits. These results show that hybridization at the tetraploid level can generate vigorous and productive recombinants with a high potential to produce promising transgressive segregants. This breeding strategy appears highly promising, supporting further research on the potential of interspecific hybridization in this group.

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

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

Delineating the elusive BaMMV resistance gene rym15 in barley by medium-resolution mapping

Barley mild mosaic virus (BaMMV), transmitted by the soil-borne protist Polymyxa graminis, has a serious impact on winter barley production. Previously, the BaMMV resistance gene rym15 was mapped on chromosome 6HS, but the order of flanking markers was non-collinear between different maps. To resolve the position of the flanking markers and to enable map-based cloning of rym15, two medium-resolution mapping populations Igri (susceptible) × Chikurin Ibaraki 1 (resistant) (I × C) and Chikurin Ibaraki 1 × Uschi (susceptible) (C × U), consisting of 342 and 180 F2 plants, respectively, were developed. Efficiency of the mechanical inoculation of susceptible standards varied from 87.5 to 100% and in F2 populations from 90.56 to 93.23%. Phenotyping of F2 plants and corresponding F3 families revealed segregation ratios of 250 s:92r (I × C, χ2 = 0.659) and 140 s:40r (C × U, χ2 = 0.741), suggesting the presence of a single recessive resistance gene. After screening the parents with the 50 K Infinium chip and anchoring corresponding SNPs to the barley reference genome, 8 KASP assays were developed and used to remap the gene. Newly constructed maps revealed a collinear order of markers, thereby allowing the identification of high throughput flanking markers. This study demonstrates how construction of medium-resolution mapping populations in combination with robust phenotyping can efficiently resolve conflicting marker ordering and reduce the size of the target interval. In the reference genome era and genome-wide genotyping era, medium-resolution mapping will help accelerate candidate gene identification for traits where phenotyping is difficult.

Factors Affecting the Efficiency of Teaching Process in Higher Education in the Republic of Serbia during COVID-19

From the moment the Republic of Serbia declared a state of emergency in the summer semester of 2019/2020, higher education institutions (HEIs) used various teaching models from Distance Learning Systems (DLS), online platforms and modern information and communication technologies (ICT), to sending materials via student e-mails and notifications via faculty portals. Using survey research as a method, the paper describes the experiences of teachers and associates at HEIs in Serbia (780 respondents) regarding the efficiency of provided education services. In this article, we used the method of content analysis and participatory observation, as well. We analysed the attitudes of teachers and associates apropos the efficiency of providing educational services through the work from home (WFH) model and distance learning (DL) and other models used in response to COVID-19 epidemiological measures in education. During the WFH setup, we looked for factors that affect educational efficiency. When it comes to the statistical technique, factor analysis was selected. Technology, managerial support, and work–home conflict are all expected to impact process efficiency, so these were the first criteria considered when selecting potential factors. Principal Component Analysis (PCA) was used as the extraction method, and the Varimax rotation method was also used. We discarded all factors with eigenvalues below one. Four factors caught our attention: School management support, Family–work conflict, Home infrastructure, and Technology choice. The results showed that F1 (School management support) is positively correlated to F2 (Family–work conflict) and efficiency and negatively correlated to F3 (Home infrastructure). Conversely, F2 is negatively correlated to F3 and positively correlated to efficiency. The F4 factor shows no significant correlations to other factors.

Identification and molecular mapping of a major quantitative trait locus underlying branch angle in soybean.

A major quantitative trait locus (QTL) modulating soybean (Glycine max) branch angle was identified by linkage analysis using two bi-parental mapping populations with and without pedigree from wild soybean (Glycine soja). Soybean branch angle is a critical architectural trait that affects many other traits of agronomic importance associated with the plant's productivity and grain yield and is thus a vital consideration in soybean breeding. However, the genetic basis for modulating this important trait in soybean and many other crops remain unknown. Previously, we developed a recombinant inbred line (RIL) population derived from a cross between a domesticated soybean (Glycine max) variety, Williams 82, and a wild soybean (Glycine soja) accession, PI 479,752, and observed drastic variation in plant architecture including branch angle among individual RILs. In this study, one of the RILs possessing extremely wide branch angle (WBA) was crossed with an elite soybean cultivar (LD00-3309) possessing narrow branch angle (NBA) to produce an F2 population composed of 147 plants and F2-derived F3 families for inheritance analysis and QTL mapping. We found that branch angle is controlled by a major QTL located on chromosome 19, designated qGmBa1 and that WBA-derived from the wild soybean accession-is dominant over NBA. This locus was also detected as a major one underlying branch angle by QTL mapping using a subset of the soybean nested association mapping (SoyNAM) population composed of 140 RILs, which were derived from a cross between a landrace, PI 437169B, possessing WBA and an elite variety, IA3023, possessing NBA. Molecular markers located in the QTL region defined by both mapping populations can be used for marker-assisted selection of branch angle in soybean breeding.

Bt Cry1Ac resistance in Trichoplusia ni is conferred by multi-gene mutations

The three-domain Cry toxin Cry1Ac from Bacillus thuringiensis （Bt） is an important insecticidal toxin in Bt sprays and has been used in transgenic Bt-crops to confer insect resistance. The cabbage looper, Trichoplusia ni, has developed resistance to Bt sprays in commercial greenhouses, and the resistance to Cry1Ac has been previously identified to be associated with altered expression of the APN1 and APN6 genes and be genetically linked to a locus on chromosome 15. In this study, the Cry1Ac resistance locus in T. ni was further finely mapped, and the specific Cry1Ac resistance-conferring mutation in the resistance locus was identified to be a 4 bp frameshift insertion in the ABCC2 gene by whole genome resequencing, midgut transcriptome analysis, candidate gene cDNA sequencing and mutation site genomic DNA sequencing. By CRISPR/Cas9 mutagenesis, a series of ABCC2 and ABCC3 mutant T. ni strains were generated, and the role of ABCC2 in the toxicity of Cry1Ac in T. ni was confirmed. The results from this study also showed that knockout of ABCC2 in T. ni conferred resistance to Cry1Ac at a level lower than that in the greenhouse-derived resistant T. ni strain and that the Cry1Ac resistance-associated alteration of APN1 and APN6 expression was independent of ABCC2 gene mutations, indicating that the altered expression of APN1 and APN6 was controlled by another gene mutation in Cry1Ac resistant T. ni. Furthermore, T. ni larval bioassays showed that the level of Cry1Ac resistance in F1 families from reciprocal crosses of the Cry1Ac resistant strain with an ABCC2 knockout CRISPR strain was significantly higher than that in ABCC2 knockout strain, indicating the presence of additional Cry1Ac resistance-conferring mutation(s) in the Cry1Ac resistant strain. Therefore, the resistance to Cry1Ac in T. ni is conferred by a mutation in ABCC2 and an additional mutation (or mutations) which leads to altered expression of APN1 and APN6. The additional Cry1Ac resistance mutation or mutations remain to be identified.

A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp (Cyprinus carpio).

Feed conversion efficiency (FCE) is an economically crucial trait in fish, however, little progress has been made in genetics and genomics for this trait because phenotypes of the trait are difficult to measure. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,416 SNP markers for common carp (Cyprinus carpio) based on high throughput genotyping with the carp 250K single nucleotide polymorphism (SNP) array in a full-sib F1 family of mirror carp (Cyprinus carpio) consisting of 141 progenies. The linkage map contained 11,983 distinct loci and spanned 3,590.09 cM with an average locus interval of 0.33 cM. A total of 17 QTL for the FCE trait were detected on four LGs (LG9, LG20, LG28, and LG32), explaining 8.9–15.9% of the phenotypic variations. One major cluster containing eight QTL (qFCE1-28, qFCE2-28, qFCE3-28, qFCE4-28, qFCE5-28, qFCE6-28, qFCE7-28, and qFCE8-28) was detected on LG28. Two clusters consisting of four QTL (qFCE1-32, qFCE2-32, qFCE3-32, and qFCE4-32) and three QTL (qFCE1-20, qFCE2-20, and qFCE3-20) were detected on LG32 and LG20, respectively. Nine candidate genes (ACACA, SCAF4, SLC2A5, TNMD, PCDH1, FOXO, AGO1, FFAR3, and ARID1A) underlying the feed efficiency trait were also identified, the biological functions of which may be involved in lipid metabolism, carbohydrate metabolism, energy deposition, fat accumulation, digestion, growth regulation, and cell proliferation and differentiation according to GO (Gene Ontology). As an important tool, high-density and high-resolution genetic linkage maps play a crucial role in the QTL fine mapping of economically important traits. Our novel findings provided new insights that elucidate the genetic basis and molecular mechanism of feed efficiency and the subsequent marker-assisted selection breeding in common carp.

Genome-wide analysis of acute low salinity tolerance in the eastern oyster Crassostrea virginica and potential of genomic selection for trait improvement.

As the global demand for seafood increases, research into the genetic basis of traits that can increase aquaculture production is critical. The eastern oyster (Crassostrea virginica) is an important aquaculture species along the Atlantic and Gulf Coasts of the United States, but increases in heavy rainfall events expose oysters to acute low salinity conditions, which negatively impact production. Low salinity survival is known to be a moderately heritable trait, but the genetic architecture underlying this trait is still poorly understood. In this study, we used ddRAD sequencing to generate genome-wide single-nucleotide polymorphism (SNP) data for four F2 families to investigate the genomic regions associated with survival in extreme low salinity (<3). SNP data were also used to assess the feasibility of genomic selection (GS) for improving this trait. Quantitative trait locus (QTL) mapping and combined linkage disequilibrium analysis revealed significant QTL on eastern oyster chromosomes 1 and 7 underlying both survival and day to death in a 36-day experimental challenge. Significant QTL were located in genes related to DNA/RNA function and repair, ion binding and membrane transport, and general response to stress. GS was investigated using Bayesian linear regression models and prediction accuracies ranged from 0.48 to 0.57. Genomic prediction accuracies were largest using the BayesB prior and prediction accuracies did not substantially decrease when SNPs located within the QTL region on Chr1 were removed, suggesting that this trait is controlled by many genes of small effect. Our results suggest that GS will likely be a viable option for improvement of survival in extreme low salinity.

Introgression of bruchid (Zabrotes subfasciatus) resistance into small red common bean (Phaseolus vulgaris) background and validation of the BRU_00261 (snpPV0007) resistance marker.

Bruchids are a major storage pest of common bean. Genetic resistance is a suitable method to avoid grain losses during storage. The objective of the study was to introgress the arcelin‐based resistance locus into selected advanced breeding line and to validate the molecular marker BRU_00261. A total of 208 progeny F4 families were phenotyped using a randomized complete block design, with three replications. Highly significant differences (P < .001) among the entries, parents and offspring were recorded for almost all traits. There was no significant difference between the two parents in the number of eggs laid. The progenies were grouped as highly resistant (34.3%), resistant (11.9%), moderately resistant (21.4%) and susceptible (32.4%). The levels of broad sense heritability ranged from 68.5%–93.9% for all the traits. Eighty‐three most resistant lines and the parental lines were genotyped with the marker BRU_00261 (snpPV0007). The marker segregation deviated significantly from the expected independent segregation towards a strong enrichment for the resistant marker in the selected families. This marker will be useful for selecting promising materials in early generations and phenotypic confirmation of positive lines in later generations.

Environmental and Genetic Factors Affecting Apospory Expressivity in Diploid Paspalum rufum.

In angiosperms, gametophytic apomixis (clonal reproduction through seeds) is strongly associated with polyploidy and hybridization. The trait is facultative and its expressivity is highly variable between genotypes. Here, we used an F1 progeny derived from diploid apomictic (aposporic) genotypes of Paspalum rufum and two F2 families, derived from F1 hybrids with different apospory expressivity (%AES), to analyze the influence of the environment and the transgenerational transmission of the trait. In addition, AFLP markers were developed in the F1 population to identify genomic regions associated with the %AES. Cytoembryological analyses showed that the %AES was significantly influenced by different environments, but remained stable across the years. F1 and F2 progenies showed a wide range of %AES variation, but most hybrids were not significantly different from the parental genotypes. Maternal and paternal genetic linkage maps were built covering the ten expected linkage groups (LG). A single-marker analysis detected at least one region of 5.7 cM on LG3 that was significantly associated with apospory expressivity. Our results underline the importance of environmental influence in modulating apospory expressivity and identified a genomic region associated with apospory expressivity at the diploid level.

A high-density linkage map and sex-linked markers for the Amazon Tambaqui Colossoma macropomum

BackgroundTambaqui (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.ResultsIn 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%.ConclusionsThe 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.

Genetic Analysis of Yield and Quality Characteristics in Provitamin A Hybrid Cassava Families in Ghana

Cassava is the most widely cultivated and consumed crop in Ghana. Malnutrition is endemic in cassava-producing regions of Africa, partly due to the low micronutrient content of this crop. The aim of this study was to generate genetic information on characteristics such as total carotenoid content, dry matter content, root weight and number, and cassava mosaic disease (CMD), and their possible combination in cassava clones, using a North Carolina II breeding scheme. Five genetically diverse yellow-fleshed clones at advanced selection stages, with CMD resistance, were used as females and two high dry matter content white-fleshed clones, selected from farmers’ fields in Ghana, were used as males. Ten F1 families were generated, and evaluated at two locations in Ghana. General combining ability (GCA) mean squares were larger than specific combining ability (SCA) mean squares for harvest index, CMD, and carotenoid content, indicating additive genetic effects. The positive significant correlations that were observed between pulp color and carotenoid content; carotenoid content and CMD; pulp color and CMD; and pulp color and cortex color, make the screening of large numbers of progenies possible in the cassava breeding program. This could allow breeders to combine carotenoid content and CMD at the early breeding stages through visual assessment of pulp color and CMD symptoms. Large numbers of genotypes can be evaluated and a few can be selected to be quantified for carotenoid content at later stages of the breeding program, to save costs. One of the parents (P6), showed positive GCA effects for carotenoid content, dry matter content, CMD and storage root weight, hence could be used as a parent to generate clones that combine carotenoid content and dry matter content.