F3 Families Research Articles

Genetic analysis of Vicia faba L.: Advancements, hereditary traits, and correlations in ‘Sakha 3’ × ‘Nubaria 3’

Genetic diversity, heritability, and genetic advance are crucial considerations in the field of plant breeding. This research aimed to evaluate these factors for traits related to yield in faba bean (Vicia faba L.), specifically focusing on the F3 and F4 generations resulting from the cross between ‘Sakha 3’ and ‘Nubaria 3’. In the initial season (2021/ 2022), 200 families from each F3 population were cultivated with specific spacing, and selection criteria included seed yield per plant (SYP) and the number of pods per plant (NPP). Top-performing plants were identified for the second cycle of pedigree selection. In the following season (2022/2023), the F4 families were arranged in a randomised complete block design. Traits like the number of branches per plant (NBP), NPP, SYP, and seed index (SI) showed substantial phenotypic and genotypic coefficients of variation, indicating their noteworthy variation. Phenotypic and genotypic correlation analyses showed positive associations between SYP and the NBP and NPP. Additionally, path coefficient analysis indicated that these traits had high positive direct effects on SYP. This research provides valuable insights into the genetic variability, heritability, and selection parameters for yield-related traits in faba bean, offering a foundation for future breeding programs aimed at improving yield and productivity.

Salt tolerance candidate genes identified by QTL mapping, RNA-seq, and functional analysis in tilapia

Salt tolerance in fish is crucial for aquaculture as it enhances survival and productivity in varying salinity conditions, thus expanding the range of viable farming environments and improving economic sustainability. Through QTL mapping and GWAS in a hybrid F2 family of Mozambique and Nile tilapia, two large-effect QTL on chromosomes 11 and 18 were identified respectively. These two QTL explained a total of 39.9 % of the phenotypic variance. The identification of a QTL on LG11 suggests the presence of a previously unrecognized genetic factor contributing to salt tolerance. Comparative transcriptomic analysis of gill and kidney tissues between susceptible and tolerant tilapias highlights the importance of osmotic balance in regulation of salt tolerance in tilapia. Integration of QTL and RNA-seq data identified two candidate genes: acyl-coenzyme A thioesterase 5 (acot5) and sodium- and chloride-dependent taurine transporter (slc6a6) likely playing critical roles in such process. Functional analysis showed that over-expressing acot5 or slc6a6 in grouper kidney cells increased viability under salt stress by 4.46 % and 17.53 %, respectively. Subcellular localization revealed nuclear presence of ACOT5 and stress-induced nuclear translocation of SLC6A6. These findings highlight acot5 and slc6a6 as candidates for genetic manipulation and selection to enhance salt tolerance in tilapia, guiding genetic improvement efforts and promoting sustainable practices.

Genetic Analysis for Seed Yield and Yield‐Related Traits in Tepary Bean (Phaseolus acutifolius A. Gray) Under Drought‐Stress and Non‐stress Conditions

ABSTRACTTepary bean (Phaseolus acutifolius A. Gray) is an under‐utilized genetic resource with significant potential for food security and stress tolerance breeding. Expanding its cultivation in southern Africa requires high‐yielding, locally adapted and drought‐tolerant varieties. This study determined the combining ability and genetic components for seed yield and related traits in tepary bean genotypes under non‐stress (NS) and drought‐stress (DS) conditions. Seven parents were selected through rigorous phenotyping and crossed using a half‐diallel design. The 7 parents and 21 F2 progenies were evaluated in 2021/2022 season at Kasinthula and Bunda sites in Malawi under NS and DS conditions using a 4 × 7 lattice design with three replications. The specific combining ability (SCA) × location interaction effect was significant (p < 0.05) for DTF, NPP, and SY, suggesting that the genetic effects of crosses were influenced by the test locations. General combining ability (GCA) and SCA mean squares were significant for the number of seeds per pod (NSP) and SY under DS conditions, indicating both additive and non‐additive gene effects. Baker's ratio (BR) > 0.50 for NPP and NSP under DS conditions suggested a preponderance of additive gene effects. G40145, G40148 and G40150 parental lines were good combiners for NPP and SY. The F2 families from crosses such as Zimbabwe landrace/G40138, Zimbabwe landrace/G40150, G40059/G40145, G40059/G40148, G40138/G40150 and G40145/G40150 were identified as best specific combiners, with enhanced SY of 1.67 t/ha under DS conditions. The study recommends advancing high‐performing early‐generation families for selection across representative environments to facilitate variety release and commercialization.

Assessment of genetic variability, heritability and correlation in advanced breeding lines of bread wheat (Triticum aestivum) under heat stress condition

Abstract An experiment was conducted under normal (with six irrigation during crop period) and stressed condition during Rabi 2019 in All India Coordinated Research Project (AICRP) on Wheat, MARS, Dharwad, Karnataka with the view of assessing genetic variability, heritability and expected genetic advance in 104 F4 families of the cross HD2864 × DBW14. The progenies exhibited wide range of variation for all the traits indicating the presence of enough genetic variability in the material under study. Under timely sown condition, the traits like leaf waxyness, NDVI at different stages, SPAD at different stages, number of productive tillers per plant, seeds per spike, grain filling duration, spike length, thousand grains weight and seed set percentage showed high variability. The traits like plant height, canopy temperature at different stages and membrane stability index showed low variability. Under late sown condition, the traits like leaf waxyness, plant height, NDVI at different stages, SPAD at different stages, number of productive tillers per plant, seeds per spike, yield per plant, row bulk yield and seed set percentage showed high variability. The traits like days to maturity, spike length and membrane stability index showed low variability. The findings shows that all traits related to crop yield are positively linked, except for canopy temperature at different growth stages. Promising lines identified through Heat susceptibility index (HSI) and Heat tolerance index (HTI) can be utilized in future breeding programs to enhance crop productivity. Keywords: Variability, Coefficient of variation, Heritability, Genetic advance.

Grain Appearance Quality of Parental and \(F_2\) Segregating Populations of Aus Rice (Oryza sativa L.)

Longer grain length with smaller grain breadth, length-breadth ratio and 1000-grain weight is considered desirable character for the development of fine grain premium quality rice. In the present experiment, grain appearance quality of 15 F2 families and 10 parental genotypes were determined to select fine grain rice. The maximum mean value for thousand seed weight was found from the genotypes P2 (29.32g), P1 (28.89g), and F2 generations of P2 x P5 (32.77g), P2 x P1 (27.30g), P1 x P4 (26.04g) and were considered as high yielders in terms of grain weight. The highest mean values for grain length were found from the genotypes P6 (9.95 mm; grain breadth 2.23 mm), P7 (9.36 mm; grain breadth 2.62 mm), and F2 generations of P6 x P7 (9.46 mm; grain breadth 2.44 mm), P3 x P6 (9.40 mm; grain breadth 2.18 mm), P7 x P6 (9.37 mm; grain breadth 2.29 mm), P7 x P3 (9.36 mm; grain breadth 2.33 mm). The F2 progenies of the cross P1 x P4 (7.79 to 11.61 mm) and P6 x P3 (7.69 to 11.11 mm) showed extremes performance for grain length indicating transgressive segregation for this trait. The superior genotypes with desirable grain characters could be selected from transgressive segregation of F2 families for the development of new varieties of fine grain rice.

The genetic basis of divergent melanic pigmentation in benthic and limnetic threespine stickleback

Pigmentation is an excellent trait to examine patterns of evolutionary change because it is often under natural selection. Benthic and limnetic threespine stickleback (Gasterosteus aculeatus) exhibit distinct pigmentation phenotypes, likely an adaptation to occupation of divergent niches. The genetic architecture of pigmentation in vertebrates appears to be complex. Prior QTL mapping of threespine stickleback pigmentation phenotypes has identified several candidate loci. However—relative to other morphological phenotypes (e.g., spines or lateral plates)—the genetic architecture of threespine stickleback pigmentation remains understudied. Here, we performed QTL mapping for two melanic pigmentation traits (melanophore density and lateral barring) using benthic-limnetic F2 crosses. The two traits mapped to different chromosomes, suggesting a distinct genetic basis. The resulting QTLs were additive, but explained a relatively small fraction of the total variance (~6%). QTLs maps differed by F1 family, suggesting variation in genetic architecture or ability to detect loci of small effect. Functional analysis identified enriched pathways for candidate loci. Several of the resulting candidate loci for pigmentation, including three loci in enriched pathways (bco1, sulf1, and tyms) have been previously indicated to affect pigmentation in other vertebrates. These findings add to a growing body of evidence suggesting pigmentation is often polygenic.

<i>SiDREB2</i>-based SNAP Marker-Assisted and Multi-Trait Selection in The Early Generation of Foxtail Millet (<i>Setaria italica</i> L. Beauv.)

Setaria italica L. or foxtail millet is known for its nutritious grains and adaptability to unfavorable environmental conditions. High productivity, early heading, medium stature, and tolerance to drought- or salinity stress are among the breeding objectives for foxtail millet. The objective of this study was to select F3 families of foxtail millet from the cross of Botok-10xICERI-6 by weighted selection index and assisted by SiDREB2-based SNAP marker. Genotyping of 178 F3 families using the SiDREB2-based SNAP marker resulted in 29 A/A genotypes, 121 A/G genotypes, and 28 G/G genotypes. Further evaluation was conducted on 48 F3 families consisting of 27 A/A genotypes and 21 A/G genotypes in an augmented randomized complete block design together with their parental genotypes (Botok-10xICERI-6) and three check genotypes (Mauliru-2, NTB-1, and Toraja). Plant height and heading time had high broad-sense heritability, whereas grain weight per plant had a moderate broad-sense heritability. Ten potential F3 families were selected based on a weighted selection index with 20% intensity, comprised of seven A/G genotypes and three A/A genotypes with a weighted selection index ranging from 0.84 to 3.76. The F3 family with pedigree numbers B10I6-15-136, B10I6-15-161, and B10I6-15-70 with A/A genotypes are considered putative transgressive segregants and could be continued to the next generation for further breeding process.

Field evaluation of UASD Bt-cotton Event-78 based early segregating generations for cotton leaf hopper

UASD Bt cotton Event-78 based early segregating generations (F2 & F3) derived from three diverse crosses were evaluated for field incidence of cotton leaf hopper during kharif-2021 & 2022 at Agricultural Research Station, UAS, Dharwad. A total 600 F2 plants from the crosses viz., UASD Bt-78 х DHS-29, UASDBt-78 х Suvin and Suvin х UASD Bt-78 were screened of which 103,100 and 102 plants respective to the three crosses were found to be resistant. The segregation of F2 population for the jassid tolerance deciphered the implicit “Inhibitory epistasis” mechanism of host plant resistance. Further evaluation of F3 families of these crosses leads to identification of 103 resistant lines from all the three crosses, the mean leafhopper population ranges from 0.67- 2.67 leafhoppers / 3 leaves with the LHRI score of 1.

Correlations among New Mexico pod‐type green chile (Capsicum annuum) fruit morphology characteristics with destemming force

AbstractDestemming refers to the removal of the calyx and pedicel from chile (Capsicum annuum) fruit, and destemming force is the amount of force required to accomplish this removal. The objective of this study was to describe the relationship between destemming force and fruit width, fruit length, and pericarp thickness, along with the genetic potential for combining the easy‐destemming attribute with the preferred fruit morphology of New Mexico (NM) pod‐type green chile. This investigation will define optimal selection criteria for reducing destemming force, while preserving the distinctive morphology of NM pod‐type green chile. We quantified phenotypic and genetic variation of 285 F3 families from three populations developed from reciprocal crosses between three NM pod‐type cultivars and an easy‐destemming cultivar. The results show destemming force exhibited significant positive phenotypic correlations with pericarp thickness and fruit width (0.90 and 0.92, respectively) and fruit length (0.69). Genetic correlations for each of the three populations for fruit morphological traits ranged from 0.2 to 0.9, with pericarp thickness with the highest genetic correlation with destemming force. Narrow‐sense heritability values were between 0.2 and 0.8, with destemming force and fruit length consistently having higher narrow‐sense heritability values. These findings suggest a correlation between the expression of pericarp thickness and destemming force. The lower estimates for pericarp thickness indicate environmental influences may play a more significant role in determining trait expression. The information generated from this study will aid in the development of efficient cultivars suited for mechanical harvesting in NM pod‐type breeding programs.

Mapping the genetic basis for sex determination and growth in hybrid tilapia (Oreochromis mossambicus × O. niloticus)

Tilapia growth and sex are key traits for aquaculture. Elucidating their molecular mechanisms can enable molecular breeding and accelerate genetic gain. To uncover the genetic basis underlying these traits for molecular breeding, we generated an F2 family by crossing Mozambique and Nile tilapia. The growth and sex traits of 284 F2 fish were recorded at 150 days post hatch. These F2 individuals exhibited sexual dimorphism in weight, body shape, and lip thickness, and were genotyped with RAD-sequencing. A high-density linkage map, consisting of 22 linkage groups with 38,102 SNPs was constructed. Association mapping revealed that QTL containing the amhy gene from male Nile tilapia largely determined sex, modulated by minor-effect loci. For growth-related traits, QTL and association analyses discovered that body weight or total length was predominantly controlled by a large-effect locus, while body shape was determined by several minor-effect loci. Analysis of transcriptomics in the liver and muscle identified novel candidate genes, including dusp2, rtn4r, bhmt1, adamts12 and s100p, for growth. These findings provide tools for sex-specific molecular breeding and valuable information for understanding the genomic architecture of growth and body shape variation. Assessing the sex-specific effects on growth can further refine selective breeding in aquaculture.

Rice breeding for multi‐canopy system: Estimations of genetic parameters and response to selection

AbstractOne strategy currently being developed to increase rice (Oryza sativa L.) productivity is using a multi‐canopy cropping system in rice cultivation. This method involves planting tall and short rice genotypes in the same hill. The objective of this experiment was to estimate the genetic parameters and response to selection in multi‐canopy rice. Each experiment was arranged in an augmented randomized complete block design with five replications for the checks. In the first planting season, 200 F3 families from IPB196 and IPB197 populations were planted in monoculture and multi‐canopy as the short genotypes. IPB187‐F‐40‐1‐1 was used in multi‐canopy as the tall genotype. Selection of 25% based on grain weight per hill of short genotype in multi‐canopy was performed, and 50 families were selected and their F4 seeds were planted in the second season along with the same tall genotype. The results indicated the genotype × cropping system was significant for grain weight per hill in the F3 and F4 generations. Grain weight per hill has a similar realized h2ns in the multi‐canopy (0.58) with monoculture (0.54). Meanwhile, the response to selection in multi‐canopy (3.60) was higher compared to monoculture (2.09), and therefore the selection of rice lines for a multi‐canopy system should be conducted in the multi‐canopy environment. A selection percentage of 5% resulted in a higher response to selection. These findings may provide insight into the acceleration of breeding rice varieties for the multi‐canopy system.

Inheritance and Response to Selection for Seed Weight Using the Large Seeded Landrace Oman 2 of Lucerne

Seed weight in lucerne (Medicago sativa) may affect subsequent seedling vigour and stand establishment. A landrace of lucerne (Oman 2) from Oman has a 100-seed weight over 60% larger than the largest seeded parent used in previous studies. Crosses were made between Oman 2 and the smaller-seeded cultivar Titan 9, and segregating families were produced for genetic analysis and measurement of response to selection for seed size. There were significant differences in 100-seed weights between the parents (Oman 2 and Titan 9) and subsequent families. Regression of 100-seed weights of F2 families versus F1 parents was highly significant (p < 0.001), as well as 100-seed weights of the F3 families versus F1 parents. Analysis of diallel crossing among large and small-seeded F1 plants revealed highly significant general (GCAs) and specific (SCAs) combining abilities, as well as highly significant reciprocals. The GCA effect was much greater than the SCA effect with a GCA/SCA ratio of 15.9. This large ratio agrees with the significant regression coefficients and indicates that 100-seed weight in lucerne has high heritability. The significance of reciprocals was due to a large maternal effect in which large-seeded maternal parents produced progenies with significantly larger seeds relative to small-seeded parents. These results indicate that large-seeded plants should be used as the maternal parents in crosses and for recurrent selection to increase the seed size of progenies.

Image analysis and polyphenol profiling unveil red-flesh apple phenotype complexity.

The genetic basis of colour development in red-flesh apples (Malus domestica Borkh) has been widely characterised; however, current models do not explain the observed variations in red pigmentation intensity and distribution. Available methods to evaluate the red-flesh trait rely on the estimation of an average overall colour using a discrete class notation index. However, colour variations among red-flesh cultivars are continuous while development of red colour is non-homogeneous and genotype-dependent. A robust estimation of red-flesh colour intensity and distribution is essential to fully capture the diversity among genotypes and provide a basis to enable identification of loci influencing the red-flesh trait. In this study, we developed a multivariable approach to evaluate the red-flesh trait in apple. This method was implemented to study the phenotypic diversity in a segregating hybrid F1 family (91 genotypes). We developed a Python pipeline based on image and colour analysis to quantitatively dissect the red-flesh pigmentation from RGB (Red Green Blue) images and compared the efficiency of RGB and CIEL*a*b* colour spaces in discriminating genotypes previously classified with a visual notation. Chemical destructive methods, including targeted-metabolite analysis using ultra-high performance liquid chromatography with ultraviolet detection (UPLC-UV), were performed to quantify major phenolic compounds in fruits' flesh, as well as pH and water contents. Multivariate analyses were performed to study covariations of biochemical factors in relation to colour expression in CIEL*a*b* colour space. Our results indicate that anthocyanin, flavonol and flavanol concentrations, as well as pH, are closely related to flesh pigmentation in apple. Extraction of colour descriptors combined to chemical analyses helped in discriminating genotypes in relation to their flesh colour. These results suggest that the red-flesh trait in apple is a complex trait associated with several biochemical factors.

Mapping QTLs for blight resistance and morpho-phenological traits in inter-species hybrid families of chestnut (Castanea spp.).

Chestnut blight (caused by Cryphonectria parasitica), together with Phytophthora root rot (caused by Phytophthora cinnamomi), has nearly extirpated American chestnut (Castanea dentata) from its native range. In contrast to the susceptibility of American chestnut, many Chinese chestnut (C. mollissima) genotypes are resistant to blight. In this research, we performed a series of genome-wide association studies for blight resistance originating from three unrelated Chinese chestnut trees (Mahogany, Nanking and M16) and a Quantitative Trait Locus (QTL) study on a Mahogany-derived inter-species F2 family. We evaluated trees for resistance to blight after artificial inoculation with two fungal strains and scored nine morpho-phenological traits that are the hallmarks of species differentiation between American and Chinese chestnuts. Results support a moderately complex genetic architecture for blight resistance, as 31 QTLs were found on 12 chromosomes across all studies. Additionally, although most morpho-phenological trait QTLs overlap or are adjacent to blight resistance QTLs, they tend to aggregate in a few genomic regions. Finally, comparison between QTL intervals for blight resistance and those previously published for Phytophthora root rot resistance, revealed five common disease resistance regions on chromosomes 1, 5, and 11. Our results suggest that it will be difficult, but still possible to eliminate Chinese chestnut alleles for the morpho-phenological traits while achieving relatively high blight resistance in a backcross hybrid tree. We see potential for a breeding scheme that utilizes marker-assisted selection early for relatively large effect QTLs followed by genome selection in later generations for smaller effect genomic regions.

Genetic improvement of Egyptian cotton (Gossypium barbadense L.) for high yield and fiber quality properties under semi arid conditions

Between 2016 and 2018, the Agriculture Research Center's Sakha Agriculture Research Station conducted two rounds of pedigree selection on a segregating population of cotton (Gossypium barbadense L.) using the F2, F3, and F4 generations resulting from crossing Giza 94 and Suvin. In 2016, the top 5% of plants from the F2 population were selected based on specific criteria. The superior families from the F3 generation were then selected to produce the F4 families in 2017, which were grown in the 2018 summer season in single plant progeny rows and bulk experiments with a randomized complete block design of three replications. Over time, most traits showed increased mean values in the population, with the F2 generation having higher Genotypic Coefficient of Variance (GCV) and Phenotypic Coefficient of Variance (PCV) values compared to the succeeding generations for the studied traits. The magnitude of GCV and PCV in the F3 and F4 generations was similar, indicating that genotype had played a greater role than the environment. Moreover, the mean values of heritability in the broad sense increased from generation to generation. Selection criteria I2, I4, and I5 were effective in improving most of the yield and its component traits, while selection criterion I1 was efficient in improving earliness traits. Most of the yield and its component traits showed a positive and significant correlation with each other, highlighting their importance in cotton yield. This suggests that selecting to improveone or more of these traits would improve the others. Families number 9, 13, 19, 20, and 21 were the best genotypes for relevant yield characters, surpassing the better parent, check variety, and giving the best values for most characters. Therefore, the breeder could continue to use these families in further generations as breeding genotypes to develop varieties with high yields and its components.

Mapping QTL associated with resistance to Pseudomonas syringae pv. actinidiae in kiwifruit (Actinidia chinensis var. chinensis).

Pseudomonas syringae pv. actinidiae (Psa) is a bacterial pathogen of kiwifruit. This pathogen causes leaf-spotting, cane dieback, wilting, cankers (lesions), and in severe cases, plant death. Families of diploid A. chinensis seedlings grown in the field show a range of susceptibilities to the disease with up to 100% of seedlings in some families succumbing to Psa. But the effect of selection for field resistance to Psa on the alleles that remain in surviving seedlings has not been assessed. The objective of this work was to analyse, the effect of plant removal from Psa on the allele frequency of an incomplete-factorial-cross population. This population was founded using a range of genotypically distinct diploid A. chinensis var. chinensis parents to make 28 F1 families. However, because of the diversity of these families, low numbers of surviving individuals, and a lack of samples from dead individuals, standard QTL mapping approaches were unlikely to yield good results. Instead, a modified bulk segregant analysis (BSA) overcame these drawbacks while reducing the costs of sampling and sample processing, and the complexity of data analysis. Because the method was modified, part one of this work was used to determine the signal strength required for a QTL to be detected with BSA. Once QTL detection accuracy was known, part two of this work analysed the 28 families from the incomplete-factorial-cross population that had multiple individuals removed due to Psa infection. Each family was assigned to one of eight bulks based on a single parent that contributed to the families. DNA was extracted in bulk by grinding sampled leaf discs together before DNA extraction. Each sample bulk was compared against a bulk made up of WGS data from the parents contributing to the sample bulk. The deviation in allele frequency from the expected allele frequency within surviving populations using the modified BSA method was able to identify 11 QTLs for Psa that were present in at least two analyses. The identification of these Psa resistance QTL will enable marker development to selectively breed for resistance to Psa in future kiwifruit breeding programs.

A high-density genetic linkage map and QTL identification for growth traits in dusky kob (Argyrosomus japonicus)

High-density genetic linkage maps provide a foundational genomic resource for quantitative trait locus (QTL) mapping, candidate gene localisation, and comparative genomic analysis. Data from such studies, in turn, can be incorporated into marker or genomics assisted selective breeding strategies for increased efficiency of aquaculture production. This study aimed to construct the first high-density genetic linkage map for dusky kob (Argyrosomus japonicus) a commercially important marine finfish in Asia, Australia, and South Africa. Using 2b-restriction site-associated DNA (2b-RAD) sequencing for genome-wide single nucleotide polymorphism (SNP) genotyping, in three full-sib F1 families (Family 1, n = 69 offspring; Family 2, n = 73 offspring; and Family 3, n = 70 offspring), led to the discovery and genotyping of 22,789 SNPs. Among these, 3992 quality filtered and informative SNPs were mapped to 24 linkage groups (LGs), aligning with the species' proposed haploid chromosome number. The total integrated genetic map spanned a length of 2550 cM with an average marker spacing of 0.68 cM, achieving a genome coverage of 98.61%. Male and female specific maps highlighted differential map lengths and recombination rates between the sexes, with the female map slightly longer and a lower recombination frequency than for the male. QTL analysis for growth-related traits, weight (W), standard length (sL), and Fulton's condition factor (K), identified a total of 25 QTLs of which five QTLs were found to be consistently shared across the traits. Collectively, these shared QTLs explained a substantial proportion of the phenotypic variance, accounting for between 9.30 and 19.30% of the observed variation, suggesting potential major genes for growth. These QTL regions led to the discovery of 65 potential candidate genes, including 11 genes that were specifically located within the shared QTLs. These genes were linked to essential biological processes, including metabolism, immunity, stress response, development, and vascular function. The establishment of this high-density genetic linkage map represents an important genomic resource for comprehending the genetic determinants of economically important traits in A. japonicus, with implications for advancing and optimising ongoing marker-assisted selection (MAS) initiatives in the species.

Expansion and improvement of ChinaMu by MuT-seq and chromosome-level assembly of the Mu-starter genome.

ChinaMu is the largest sequence-indexed Mutator (Mu) transposon insertional library in maize (Zea mays). In this study, we made significant improvements to the size and quality of the ChinaMu library. We developed a new Mu-tag isolation method Mu-Tn5-seq (MuT-seq). Compared to the previous method used by ChinaMu, MuT-seq recovered 1/3 more germinal insertions, while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental time. Using MuT-seq, we identified 113,879 germinal insertions from 3,168 Mu-active F1 families. We also assembled a high-quality genome for the Mu-active line Mu-starter, which harbors the initial active MuDR element and was used as the pollen donor for the mutation population. Using the Mu-starter genome, we recovered 33,662 (15.6%) additional germinal insertions in 3,244 (7.4%) genes in the Mu-starter line. The Mu-starter genome also improved the assignment of 117,689 (54.5%) germinal insertions. The newly upgraded ChinaMu dataset currently contains 215,889 high-quality germinal insertions. These insertions cover 32,224 pan-genes in the Mu-starter and B73Ref5 genomes, including 23,006 (80.4%) core genes shared by the two genomes. As a test model, we investigated Mu insertions in the pentatricopeptide repeat (PPR) superfamily, discovering insertions for 92% (449/487) of PPR genes in ChinaMu, demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.

Quality assessment of flax advanced breeding lines varying in seed coat color and their potential use in the food and industrial applications

BackgroundWith the increasing consumer awareness of the strong relationship between food and health, flax became a promising functional food due to its bioactive nutraceutical composition. Intra-specific crosses of eight contrasting flax genotypes were performed previously, and within segregating F6 progeny families, we investigated a close-up composition of phytochemicals derived from whole seeds.ResultsThe considerable genetic variation among the flax F6 families suggested that intra-specific hybridization is essential in flax breeding to obtain and broaden genetic variability and largely affirmed the opportunity for selecting promising lines. Also, significant variations in the targeted metabolite contents and antioxidant properties were observed among brown and yellow-seeded families. Notably, brown-seeded families expressed the highest average values of saturated fatty acids, protein, fiber, tocopherol, phenolics, SDG, and SECO lignans. Yellow-seeded families represented the highest average content of unsaturated fatty acids and mucilage. The cultivation year significantly affects flaxseed’s composition and functional properties, presumably due to temperature, humidity, and sunshine time differences. Interestingly, the seeds obtained in warmer conditions were more potent and had more chemical constituents. The favorable genetic correlations among all evaluated traits suggest the possibility of joint genetic selection for several nutritional and phytochemical characteristics in flax. The current study highlights the importance and utilization of 19 top families as their seeds and oil play imperative roles in the pharmaceuticals and food industries. The antioxidant capacity of the seeds showed that families 84B, 23B, 35Y, 95Y, 30B, 88B, and 78B serve as a natural source of dietary antioxidants beneficial to human health. To increase the oxidative stability of the flaxseed oil, the quality evaluation identified some families with low levels of linolenic acid.ConclusionsThese findings are essential to improving flaxseed’s nutritional quality and therapeutic properties through a bulk breeding program.

Height inheritance in durum wheat (Triticum durum Desf.) hybrids with D<sub> 2</sub> and D<sub> 3</sub> hybrid dwarfing genes

Background. Durum wheat (BBAuAu, 2n=28) carries the D2 and D3 hybrid dwarfing genes. A study of the nature of D genes and a research of their influence on the adaptive and selectively valuable traits of hybrid plants with hybrid dwarfing genes is of theoretical and practical interest. It was previously established that the dominant alleles of the D2 and D3 genes significantly reduce the height of durum wheat hybrid plants and positively affect the kernel size and vitreousness. The purpose of the present work was to study the inheritance of height in hybrids obtained by crossing a semi-dwarf durum winter wheat cultivar with lines carrying hybrid dwarfing genes. Material and methods. The material of the study was four lines of durum wheat: L-961, L-962, L-963 and L-964 carrying hybrid dwarfing genes D2 and D3, a cultivar of semi-dwarf winter durum wheat ‘Krupinka’ (k-64725) with the rht1 gene, and hybrids of these lines with this cultivar. ‘Krupinka’ was used as the female parent in hybridization by controlled pollination. The degree of dominance was determined according to Beil and Atkins. Statistics were performed using the Pearson’s -x2 test. Results and conclusions. The analysis of plant lines of durum wheat with the D2 and D3 hybrid dwarfing genes showed that the average height of the ‘Krupinka’ × L-962 and ‘Krupinka’ × L-963 hybrids was 30 cm lower compared to the tall parent, the degree of dominance was 0.9 and 1.9 respectively. In hybrids with lines L-961 and L-964, there was no dominance of short stature. The height variability in F2 hybrids was continuous and prevented combining them into any phenotypic classes. The F3 families of ‘Krupinka’ × L-962 and ‘Krupinka’ × L 963 hybrids segregated by height into three phenotypic classes. The actual ratio of phenotypic classes did not contradict the theoretical one of 10:3:3. The obtained numerical ratios of F3 families are generally similar to those found in the literature. A distinctive feature is the absence of recessive alleles in D genes. It is assumed that the latter are regulators of phytohormone gene depression and do not have recessive alleles. It will be more correct to designate the observed phenotypic classes as D2D2 i and D3D3 i, where D2 i и D3 i denote homologues of chromosomes with a different number of multigenes. Conclusion. The study of height inheritance in the obtained hybrids indicated the presence of dominant D2 and D3 genes in the L-962 and L-963 lines and of the semi-dominant D3 gene in the L-961 line. A distinctive feature of height inheritance in durum wheat lines with the D2 and D3 hybrid dwarfing genes is the absence of recessive alleles in the D genes, i.e. no dominance of short stature