F1 Genotypes Research Articles

An Immortalized Genetic Mapping Population for Perennial Ryegrass: A Resource for Phenotyping and Complex Trait Mapping.

To address the lack of a truly portable, universal reference mapping population for perennial ryegrass, we have been developing a recombinant inbred line (RIL) mapping population of perennial ryegrass derived via single seed descent from a well-characterized F2 mapping population based on genetically distinct inbred parents in which the natural self-incompatibility (SI) system of perennial ryegrass has been overcome. We examined whether it is possible to create a genotyping by sequencing (GBS) based genetic linkage map in a small population of the F6 generation of this population. We used 41 F6 genotypes for GBS with PstI/MspI-based libraries. We successfully developed a genetic linkage map comprising 6074 SNP markers, placing a further 22080 presence and absence variation (PAV) markers on the map. We examined the resulting genetic map for general and RIL specific features. Overall segregation distortion levels were similar to those experienced in the F2 generation, but segregation distortion was reduced on linkage group 6 and increased on linkage group 7. Residual heterozygosity in the F6 generation was observed at a level of 5.4%. There was a high proportion of chromosomes (30%) exhibiting the intact haplotype of the original inbred parents of the F1 genotype from which the population is derived, pointing to a tendency for chromosomes to assort without recombining. This could affect the applicability of these lines and might make them more suitable for situations where repressed recombination is an advantage. Inter- and intra-chromosomal linkage disequilibrium (LD) analysis suggested that the map order was robust. We conclude that this RIL population, and subsequent F7 and F8 generations will be useful for genetic analysis and phenotyping of agronomic and biological important traits in perennial ryegrass.

Mapping of quantitative trait loci for microspore embryogenesis-related traits in the oilseed rape doubled haploid population DH4069 × Express 617

Oilseed rape (Brassica napus L.) is among dicotyledonous plants, a model species for microspore embryogenesis. Tremendous differences exist among oilseed rape genotypes in their embryogenic response and direct embryo to plant conversion. Despite some attempts to identify relevant genes, the genetic basis of these traits remains largely unknown. The objective of this work was to develop and to provide to the scientific community a doubled haploid (DH) population derived from a cross of the reported highly embryogenic genotype DH4079 and the low embryogenic inbred line Express 617. A population of 198 DH-lines was generated and genotyped with the Brassica 60 K Illumina Infinium™ SNP array. The parental and the F1 genotypes as well as between 81 and 107 DH-lines were characterized for their number of microspores, number of microspore-derived embryos, embryo survival rate, direct embryo to shoot conversion, and related traits. The results obtained for the F1 genotype were mostly in between the two parents. SNP markers in the DH population showed to 49% distorted segregation and of those 63% were in favor of DH4079. Significant genotypic differences were found for all traits and heritabilities ranged from 66 to 88%. Together, 13 quantitative trait loci (QTL) for the different traits were identified on linkage groups A01, A02, A05, A10, C04, and C06, and candidate genes were identified within their QTL confidence intervals.

Direct Testing for Allele-Specific Expression Differences Between Conditions.

Allelic imbalance (AI) indicates the presence of functional variation in cis regulatory regions. Detecting cis regulatory differences using AI is widespread, yet there is no formal statistical methodology that tests whether AI differs between conditions. Here, we present a novel model and formally test differences in AI across conditions using Bayesian credible intervals. The approach tests AI by environment (G×E) interactions, and can be used to test AI between environments, genotypes, sex, and any other condition. We incorporate bias into the modeling process. Bias is allowed to vary between conditions, making the formulation of the model general. As gene expression affects power for detection of AI, and, as expression may vary between conditions, the model explicitly takes coverage into account. The proposed model has low type I and II error under several scenarios, and is robust to large differences in coverage between conditions. We reanalyze RNA-seq data from a Drosophila melanogaster population panel, with F1 genotypes, to compare levels of AI between mated and virgin female flies, and we show that AI × genotype interactions can also be tested. To demonstrate the use of the model to test genetic differences and interactions, a formal test between two F1s was performed, showing the expected 20% difference in AI. The proposed model allows a formal test of G×E and G×G, and reaffirms a previous finding that cis regulation is robust between environments.

Kendali Genetik Karakter Morfologi dan Agronomi pada Tiga Populasi Sorgum (Sorghum bicolor (L.) Moench)

<p align="center"><strong>ABSTRACT</strong></p><p align="center"><strong> </strong></p>Sorghum is one of the potential foods with a higher protein content than rice. Sorghum seeds can be milled and cooked as sorghum rice. This study was aimed to obtain information on the inheritance of morphological and agronomic characters from the population derived from crosses of wide genetic background. The study consisted of the formation of F1 population and evaluation of morphological and agronomic characters in the segregated population (F2) of the three selected F1 genotypes. The location of the research was at IPB Experimental Field, Leuwikopo. The performance of the F1 genotypes were between the two parents, except for the yield components of PI-150-20-A x Numbu and PI-150-20-A x Kawali were higher than the parental lines. The performance of the F2 generation population was also between the parental lines, but with a wider distribution. The sorghum seed color is controlled not only by additive and dominant gene action, but also by epistatic gene action. The character of seed weight per panicle is controlled by epistatic gene action. In the F2 population of the crosses of PI-150-20-A x Numbu and PI-150-20-A x Kawali and PI-10-90-A x Numbu, the seed weight character is inherited with moderate heritability value. Based on genes action dan heritability, bulk or single seed descent method are suitable for yield improvement of the populations.<br /><br />Keywords: gene action, heritability, seed color, segregation, sorghum<br /><br /><br />

Genetic architecture of aerial and root traits in field-grown grafted grapevines is largely independent.

QTLs were identified for traits assessed on field-grown grafted grapevines. Root number and section had the largest phenotypic variance explained. Genetic control of root and aerial traits was independent. Breeding new rootstocks for perennial crops remains challenging, mainly because of the number of desirable traits which have to be combined, these traits include good rooting ability and root development. Consequently, the present study analyzes the genetic architecture of root traits in grapevine. A segregating progeny of 138 F1 genotypes issued from an inter-specific cross between Vitis vinifera cv. Cabernet-Sauvignon×V. riparia cv. Gloire de Montpellier, used as rootstock, was phenotyped in grafted plants grown for 2years in the field. Seven traits, related to aerial and root development, were quantified. Heritability ranged between 0.44 for aerial biomass to 0.7 for root number. Total root number was related to the number of fine roots, while root biomass was related to the number of coarse roots. Significant quantitative trait loci (QTLs) were identified for all the traits studied with some of them explaining approximately 20% of phenotypic variance. Only a single QTL co-localized for root and aerial biomass. Identified QTLs for aerial-to-root biomass ratio suggest that aerial and root traits are controlled independently. Genes known to be involved in auxin signaling pathways and phosphorus nutrition, whose orthologues were previously shown to regulate root development in Arabidopsis, were located in the confidence intervals of several QTLs. This study opens new perspectives for breeding rootstocks with improved root development capacities.

Genetics of bruchid (Callosobruchus maculatus Fab.) resistance in cowpea (Vigna unguiculata (L.) Walp.)

Bruchid resistance has been measured using a variety of techniques. Mean development period (MDP) and percentage adult emergence (PAE) are two of the more important traits measuring bruchid (Callosobruchus maculatus Fab.) resistance in cowpea. The objective of the study was to evaluate the genetic relationship between MDP and PAE in C. maculatus resistant cowpea. Seventy-two F2 population plants were developed from the cross between C. maculatus resistant TVu-11953 (with delayed MDP and low PAE) and C. maculatus susceptible Ife Brown (with early MDP and high PAE) which were evaluated for resistance to cowpea C. maculatus. MDP at 45 days after infestation (DAI) and PAE at 60 DAI were taken as analysed measures for resistance to C. maculatus infestation. Data generated were subjected to chi-square analysis. Varied resistant response to C. maculatus infestation was observed among the F2 generation plants but their responses showed inclination to the susceptible parent. A 15:1 ratio for susceptible to resistant genotypes was observed with MDP among the F2 genotypes evaluated which is an indication of the presence of two recessive genes that control of MDP. The segregation of PAE also showed a 15:1 ratio goodness of fit (P > 0.05) for susceptible to resistant genotypes. Test of independence between MDP and PAE was not significant (χ2 = 2.19, P = 0.19). This study revealed that the recessive genes controlling these two traits (MDP and PAE) were independently assorted and showed no linkage. This was also evident in the observed F2 genotypes with C. maculatus resistance expressing either delayed MDP or low PAE and not both in the study.

Growth performance of yearling F1 progeny of different crossbred beef cattle

Bangladesh has a great demand of beef but it has been facing demand and supply mismatches due to insufficient production and supply of beef, low carcass yield of native cattle and recent no-cattle export policy of a long bordered neighboring country. Thus, the present work was undertaken with an objective to develop market beef cattle of average >150 Kg carcass weight by 24 months with an average FCR of <6.50 under on farm feeding and management condition. Aiming at developing breeding bulls the native dams of BCB-1 (BLRI Cattle Breed 1) were inseminated with the imported frozen semen of Brahman, Simmental, Charolais and Limousin. The crossbred progeny of different assorted F1 genotypes were being selected and their production and breeding performance were evaluated and compared with BCB-1. All pregnant (> 6 months of gestation period) cows were in pre-natal care, and all calves were raised in a single plane of nutrition and management. All crossbred progeny performed better than BCB-1 in terms of live weights and average daily gains. Among the crossbreds, Charolais×BCB-1 had the highest (p<0.001) birth weight (27.5±1.52 kg) followed by Brahman×BCB-1 (24.1±1.23), Simmental×BCB-1 (21.9±1.78), Limousin×BCB-1 (19.8±1.39) and BCB-1×BCB-1 (18.4±1.09), and the genotypes differences were highly significant (p<0.001). In average growth curve, Simmental cross grew faster followed by Charolais, Limousin, Brahman crosses and purebred BCB-1. The genotype×environment interaction was only observed in birth weight. Purebred BCB-1 had the lowest daily DM intake and showed the lowest FCR in all ages compare to other crosses. Calf scour and alopecia occurred in all genotypes. In this breeding program, calf mortality was found as 5.26%. Simmental×BCB-1 is performing as the best among the five genotypes in terms of growth up to 12 month of age.Bang. J. Anim. Sci. 2017. 46 (2): 82-87

Genetic analysis of thrips resistance in cowpea (Vigna unguiculata [L.] Walp.)

Flower bud thrips, Megalurothrips sjostedti is the most severe field pest of cowpea that causes massive flower abortion which eventually results to substantial yield reduction in Africa. There is paucity of information on the mode of gene actions controlling inheritance of resistance to flower bud thrips in cowpea in the literature. The objectives of study were to assess the genetic variability for thrips resistance among the cowpea germplasm, determined the mode of inheritance of genes that conferred resistance and both broad and narrow-sense heritability estimates for the inheritance of thrips resistance in cowpea. Twelve cowpea lines were used in crosses in the screen house at IITA, Ibadan. The mating was accomplished using North Carolina design II to generate 48F1 hybrids, which were eventually evaluated with the parents. Data on number of peduncles, number of pods and number of thrips per flower were recorded and subjected to analysis of variance using random model by SAS 9.2. Significant variability was observed for most agronomic and thrip-adaptive traits among the cowpea germplasm, parental-lines and F1 genotypes evaluated. General combining ability (GCA) and specific combining ability (SCA) mean squares were significant (P < 0.01) for number of pods per plant and other traits under the research environment. The GCA effect accounted for 68.82–80.07% of the total variation among hybrids for all traits except days to flowering; SCA explained less than 50% of the total variation. Narrow-sense heritability estimates ranged from 7.53 (days to flower) to 63.92% (number of peduncles per plant). Additive gene action largely controlled the inheritance of yield components and other traits under thrips infestation and these traits were moderately heritable.

Mapping of genetic locus for leaf trichome in Brassica oleracea.

The genetic locus for leaf trichome was identified via marker-based mapping and SNP microarray assay, and a functional marker was developed to facilitate the breeding for hairiness in Brassica oleracea. Plant trichomes are involved in various functions particularly in protecting plants against some biotic and abiotic damages. In the present study, an F2 segregating population was developed from the cross between a glabrous cultivated B. oleracea (CC, 2n=18) and a hairy wild relative, B. incana (CC, 2n=18). A 1:3 segregation pattern between glabrous and hairy plants was detected among 1063 F2 genotypes, and the locus for hairiness was mapped in a 4.3-cM genetic region using 267 SSR markers among 149 F2 genotypes, corresponding to a 17.6-Mb genomic region on chromosome C01. To narrow the genetic region for hairiness, the Brassica 60K SNP Bead Chip Arrays were applied to genotype 64 glabrous and 30 hairy F2 plants, resulting in a 1.04-Mb single peak region located in the 17.6-Mb interval. A candidate gene, BoTRY, was identified by qRT-PCR which revealed significant higher expression in glabrous F2 genotypes as compared with that in hairy plants. A cleaved amplified polymorphic site marker was successfully developed to distinguish the sequence variations of BoTRY between hairy and glabrous plants. Our study will be helpful for molecular breeding for hairiness in B. oleracea.

CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome

Although CRISPR/Cas9 genome editing has provided numerous opportunities to interrogate the functional significance of any given genomic site, there is a paucity of data on the extent of molecular scars inflicted on the mouse genome. Here we interrogate the molecular consequences of CRISPR/Cas9-mediated deletions at 17 sites in four loci of the mouse genome. We sequence targeted sites in 632 founder mice and analyse 54 established lines. While the median deletion size using single sgRNAs is 9 bp, we also obtain large deletions of up to 600 bp. Furthermore, we show unreported asymmetric deletions and large insertions of middle repetitive sequences. Simultaneous targeting of distant loci results in the removal of the intervening sequences. Reliable deletion of juxtaposed sites is only achieved through two-step targeting. Our findings also demonstrate that an extended analysis of F1 genotypes is required to obtain conclusive information on the exact molecular consequences of targeting events.

Understanding the inheritance of mungbean yellow mosaic virus (MYMV) resistance in mungbean (Vigna radiata L. Wilczek)

Mungbean, Vigna radiata, third in the series of important pulse crops, still suffers from yield loss due to mungbean yellow mosaic disease caused by mungbean yellow mosaic virus (MYMV). Hence, studies on plant-microbe interaction are necessary for understanding the inheritance of resistance. This study concentrated on identification of linked molecular markers for MYMV resistance and to find the genetic inheritance of MYMV resistance in mungbean. A total of 413 germplasm entries in a MYMV hot spot area (Vamban) were subjected to natural field infection and 13 selected resistant lines were subjected to Agrobacterium infection using strains harboring partial genome of two different MYMV isolates, VA221 and VA239. Among the resistant lines, KMG189 showed strain-specific resistance to VA221 and had no symptoms during field trials. Ninety F2 genotypes were developed from the cross made between KMG189 (MYMV-resistant) and VBN(Gg)2 (MYMV-susceptible), segregated in the Mendelian single cross ratio 3S:1R; susceptibility of all the F1s to MYMV suggested that the MYMV resistance in mungbean is governed by a single recessive gene. Two SCAR markers CM9 and CM815 were developed through bulk segregant analysis, and the linkage analysis proved CM815 SCAR marker to be linked at 5.56 cM with MYMV resistance gene and SCAR CM9 had nil recombination percentage, suggesting it to be very closely linked to the MYMV resistance gene. SCAR marker CM9 was present in chromosome number 3 of mungbean suggesting novel loci for virus resistance in mungbean. The identified loci can be used for developing varieties resistant to MYMV in mungbean.

S_allele identification and genetic diversity analysis of apricot cultivars

ABSTRACTIn this study, the sexual incompatibility and S-allele diversity of 24 Turkish apricot cultivars, Paviot and Sakıt-1 as parents and 127 F1 progenies were identified by polymerase chain reaction (PCR) and sequencing techniques. Additionally, genetic diversity and relatedness among the 24 cultivars were determined using 18 simple sequence repeat (SSR) markers from the genus Prunus. PCR for S_alleles identified nine different S-RNase alleles in the 24 apricot cultivars, namely Sc, S1, S2, S8, S9, S20, S24, S52, and S53. All primers amplified only one S_allele in the cultivars Adilcevaz-1, Adilcevaz-3, Ethembey, Pasamismisi, Canakkale, and Soganci. Most of the Turkish cultivars were self-incompatible. The Sc allele was present in only three cultivars (Canakkale, Ethembey, Imrahor) that are, therefore, self-compatible. The S_alleles of cultivars Paviot and Sakıt-1 displayed homology with the Sc, S2 and S20, and S52 alleles. In the 127 F1 genotypes, the two S_alleles of Paviot were inherited by roughly half of the offspring, while about 76% of the offspring inherited the S52 allele from Sakıt-1, and less than 24% inherited S20. The amplification using all SSR 18 primers was successful and produced 128 polymorphic alleles with an average of 7.11 alleles per locus. Among the apricot cultivars studied, expected heterozygosity (He) ranged from 0.33 to 0.72, observed heterozygosity (Ho) ranged from 0.42 to 1.00, PIC values were between 0.28 and 0.89, and similarity rates were between 0.30 and 0.68. The cultivars Levent and Ozal were genetically closest (0.68) while cultivars Sakıt-3 and Sogancı were the most distinct (0.30).

Isolation and half-diallel analysis of earliness in five (vicia faba l.) Genotypes

The present investigation was carried out at Genetic Resources Department, Bahtim, Egypt, to evaluate five faba bean cultivars in Half-diallel crosses set. Ten crosses were constituted in 2014/2015 winter season, whereas, parents and crosses were evaluated in 2015/2016 winter season, in a randomized complete block design, with three replications. Results revealed highly significant variations within parents and F1 genotypes, indicating a wide genetic variability for the studied characters and the possibility of genetic improvement, using such genetic pools of faba bean. Some crosses recorded significant desired heterotic percentages relative to mid parent and better parents for all studied traits, except for plant height and numbe of branches per plant. Both general (GCA) and specific (SCA) combining abilities were significant for all studied traits, revealing the important role of both additive and dominant earliness in the inheritance of the studied characters. The ratio of general and specific combining abilities (GCA/SCA) indicated great additive effects for the majority of the studied characters. P1 and P5 were proved to be good combiners for all studied traits except for number of pods per nod and number of pods per plant. Several crosses exhibited highly significant positive SCA effects for the studied traits, especially P2×P3 and P4×P5 for number of seeds per plant, with high seed weight and number of pods per plant. Heritability, in the broad sense (H2bs%) estimates generally was, high for all studied traits, except for number of branches per plant and number of pods per nod. However, heritability, in the narrow sense, was high for 100-seed weight (72.25%) and pod length (51.03%), while, it was low for the majority of traits. High heritability values indicated that such traits would respond to selection.

Wolbachia in the Drosophila yakuba Complex: Pervasive Frequency Variation and Weak Cytoplasmic Incompatibility, but No Apparent Effect on Reproductive Isolation.

Three hybridizing species-the clade [(Drosophila yakuba, D. santomea), D. teissieri]-comprise the yakuba complex in the D. melanogaster subgroup. Their ranges overlap on Bioko and São Tomé, islands off west Africa. All three species are infected with Wolbachia-maternally inherited, endosymbiotic bacteria, best known for manipulating host reproduction to favor infected females. Previous analyses reported no cytoplasmic incompatibility (CI) in these species. However, we discovered that Wolbachia from each species cause intraspecific and interspecific CI. In D teissieri, analyses of F1 and backcross genotypes show that both host genotype and Wolbachia variation modulate CI intensity. Wolbachia-infected females seem largely protected from intraspecific and interspecific CI, irrespective of Wolbachia and host genotypes. Wolbachia do not affect host mating behavior or female fecundity, within or between species. The latter suggests little apparent effect of Wolbachia on premating or gametic reproductive isolation (RI) between host species. In nature, Wolbachia frequencies varied spatially for D. yakuba in 2009, with 76% (N=155) infected on São Tomé, and only 3% (N=36) infected on Bioko; frequencies also varied temporally in D. yakuba and D. santomea on São Tomé between 2009 and 2015. These temporal frequency fluctuations could generate asymmetries in interspecific mating success, and contribute to postzygotic RI. However, the fluctuations in Wolbachia frequencies that we observe also suggest that asymmetries are unlikely to persist. Finally, we address theoretical questions that our empirical findings raise about Wolbachia persistence when conditions fluctuate, and about the stable coexistence of Wolbachia and host variants that modulate Wolbachia effects.

Fine mapping of the chromosome 5B region carrying closely linked rust resistance genes Yr47 and Lr52 in wheat.

Fine mapping of Yr47 and Lr52 in chromosome arm 5BS of wheat identified close linkage of the marker sun180 to both genes and its robustness for marker-assisted selection was demonstrated. The widely effective and genetically linked rust resistance genes Yr47 and Lr52 have previously been mapped in the short arm of chromosome 5B in two F3 populations (Aus28183/Aus27229 and Aus28187/Aus27229). The Aus28183/Aus27229 F3 population was advanced to generate an F6 recombinant inbred line (RIL) population to identify markers closely linked with Yr47 and Lr52. Diverse genomic resources including flow-sorted chromosome survey sequence contigs representing the orthologous region in Brachypodium distachyon, the physical map of chromosome arm 5BS, expressed sequence tags (ESTs) located in the 5BS6-0.81-1.00 deletion bin and resistance gene analog contigs of chromosome arm 5BS were used to develop markers to saturate the target region. Selective genotyping was also performed using the iSelect 90K Infinium wheat SNP assay. A set of SSR, STS, gene-based and SNP markers were developed and genotyped on the Aus28183/Aus27229 RIL population. Yr47 and Lr52 are genetically distinct genes that mapped 0.4cM apart in the RIL population. The SSR marker sun180 co-segregated with Lr52 and mapped 0.4cM distal to Yr47. In a high resolution mapping population of 600 F2 genotypes Yr47 and Lr52 mapped 0.2cM apart and marker sun180 was placed 0.4cM distal to Lr52. The amplification of a different sun180 amplicon (195bp) than that linked with Yr47 and Lr52 (200bp) in 204 diverse wheat genotypes demonstrated its robustness for marker-assisted selection of these genes.

A novel mutation in exon 2 of FGB caused by c.221G>T\u2020 substitution, predicting the replacement of the native Arginine at position 74 with a Leucine (p.Arg74Leu\u2020) in a proband from a Kurdish family with dysfibrinogenaemia and familial venous and arterial thrombosis

Dysfibrinogenaemias may present in either congenital or acquired form and are disorders of fibrinogen structure which may or may not be associated with abnormal function. More than 100 point mutations with single amino acid substitutions have been identified in over 400 families. These lead to defective DNA in the translated fibrinogen molecule. Such cases have improved our understanding of the fibrinogen–fibrin structure. Six members of a consanguineous family including a female proband, a female sibling, three male siblings and a daughter, with ages between 29 years and 53 years presented with early onset venous and premature arterial thromboembolic disease were investigated for a pro-thrombotic tendency associated with dysfibrinogenaemia. The family was investigated using standard coagulation assays and DNA sequencing of the genes encoding the FGA, FGB and FGG. All cases have dysfibrinogenaemia with a fibrinogen level 1.4 to 1.5 (1.9–4.3 g/L). Thrombophilia testing (including AT, PS & PC, F5 G1691A (FV Leiden)/F2 (prothombin G20210A) genotypes, homocysteine, antiphosphlipid antibody, paroxysmal nocturnal haemoglobinuria by flow cytometry and Janus Kinase-2 (exon 14)) were normal. PCR amplification and sequencing of exon 2 of FBG revealed a heterozygous mutation for a c.221G> T†substitution, predicting the replacement of the native Arginine at position 74 with a Leucine (p.Arg74Leu†). In silico analysis of p.Arg74Leu strongly support pathogenicity. A novel mutation was identified in exon 2 of FGB caused by c.221G> T† substitution, predicting the replacement of Arginine at position 74 with a Leucine (p.Arg74Leu†) in a proband from a Kurdish family with dysfibrinogenaemia and familial venous and arterial thrombosis.

Regenerasi dan Aklimatisasi Kultur Antera Enam Persilangan F1 Padi Sawah

ABSTRACT&lt;br /&gt;&lt;br /&gt;The breeding of rainfed rice tolerant to drought can be accomplished using anther culture. The objectives of this research were to determine regeneration abilities of six F1 anther culture and its acclimatization ability. The experiment was arranged in completely randomized design with 14 replications. The treatments consisted of six F1 derived from crossing: INPARI 18 x IR83140-B-11-B (G1), INPARI 18 x B12825E-TB-1-25 (G2), INPARI 18 x IR87705-14-11-B-SKI-12 (G3), INPARI 22 x IR83140-B-11-B (G4), Bio-R81 x O18b-1 (G5), Bio-R82-2 x O18b-1 (G6). Media for callus induction was based on N6 medium + 2.0 mg L-1 NAA + 0.5 mg L-1 kinetin + 1.0 mM putresin + 60 g L-1 sucrosa, media for regeneration was based on MS + 0.5 mg L-1 NAA + 2.0 mg L-1 kinetin + 1.0 mM putresin, and media for rooting was based on MS + 0.5 mg L-1 IBA + 30 g L-1 sucrosa. The result indicated that all six F1 had different ability in anther culture. Bio-R82-2 x O18-b1 (G6) and Bio-R81 x O18-b1 (G5) F1 genotype had good response both of callus induction and plant regeneration. These two F1 genotypes also gave the highest ratio of green planlet production to number of anther inoculated (GP:AI) were 5.50% and 4.65%, respectively. In this research, there were identified doubled haploid plants were developed from 4 F1 derived cross namely G2 (2 plants), G3 (4 plants), G5 (21 plants), and G6 (26 plants).&lt;br /&gt;&lt;br /&gt;Keywords: Callus induction, doubled haploid, rice&lt;br /&gt;&lt;br /&gt;

Segregation Analysis of SSR, SNP, and AFLP Markers in F2 Population of Solanum lycopersicum × S. arcanum (Analisis Segregasi Marka SSR, SNP, dan AFLP pada Populasi F2 Persilangan Solanum lycopersicum × S. arcanum)

&lt;p&gt;Distorted marker segregation is a common phenomenon in interspecific cross of various crops. Previous mapping study of early&lt;br /&gt;blight fungus (Alternaria solani) resistance loci showed 52% marker distortion in the genetic linkage map of 176 F2 progenies&lt;br /&gt;derived from Solanum lycopersicum cv. Solentos × S. arcanum LA2157. The objectives of this study were to analyze in detail the&lt;br /&gt;marker segregation in the map and to determine the cause of segregation distortion by calculating the allele and genotype&lt;br /&gt;frequencies of each marker. Out of 371 mapped markers, 192 markers deviated from the expected Mendelian ratio of 1 : 2 : 1.&lt;br /&gt;Distorted markers occurred in all chromosomes, ranging from 1% to 92%. Surplus of S. arcanum homozygotes contributed most&lt;br /&gt;to the skewness (40%), followed by heterozygotes (18%), and S. lycopersicum homozygotes (5%). The allele frequencies of 152&lt;br /&gt;markers deviated from the expected allele homogeneity frequency, indicating that their segregation might be affected by&lt;br /&gt;gamethophytic selection. Sixty-one markers deviated from the expected F2 genotype frequency distribution, indicating that their&lt;br /&gt;segregation might be influenced by zygotic selection. Thirty-seven of the distorted markers showed deviation from expected&lt;br /&gt;frequencies of allele homogeneity and F2 genotype frequency distribution. Distorted markers can be retained in linkage analysis&lt;br /&gt;since chromosomal regions containing distorted markers showed linkage with early blight fungus resistance loci. Further&lt;br /&gt;identification of the mechanism contributing segregation distortion requires detailed and extensive mapping studies.&lt;/p&gt;

A Robertsonian translocation from Thinopyrum bessarabicum into bread wheat confers high iron and zinc contents

AbstractDevelopment of wheat–alien translocation lines has facilitated practical utilization of alien species in wheat improvement. The production of a compensating Triticum aestivum–Thinopyrum bessarabicum whole‐arm Robertsonian translocation (RobT) involving chromosomes 6D of wheat and 6Eb of Th. bessarabicum (2n = 2x = 14, EbEb) through the mechanism of centric breakage–fusion is reported here. An F2 population was derived from plants double‐monosomic for chromosome 6D and 6Eb from crosses between a DS6Eb(6D) substitution line and bread wheat cultivar ‘Roushan’ (2n = 6x = 42, AABBDD) as female parent. Eighty F2 genotypes (L1–L80) were screened for chromosome composition. Three PCR‐based Landmark Unique Gene (PLUG) markers specific to chromosomes 6D and 6Eb were used for screening the F2 plants. One plant with a T6EbS.6DL centric fusion (RobT) was identified. A homozygous translocation line with full fertility was recovered among F3 families and verified with genomic in situ hybridization (GISH). Grain micronutrient analysis showed that the DS6Eb(6D) substitution line and T6EbS.6DL stock have higher Fe and Zn contents than the recipient wheat cultivar ‘Roushan’.

Epistatic partners of neurogenic genes modulate Drosophila olfactory behavior.

The extent to which epistasis affects the genetic architecture of complex traits is difficult to quantify, and identifying variants in natural populations with epistatic interactions is challenging. Previous studies in Drosophila implicated extensive epistasis between variants in genes that affect neural connectivity and contribute to natural variation in olfactory response to benzaldehyde. In this study, we implemented a powerful screen to quantify the extent of epistasis as well as identify candidate interacting variants using 203 inbred wild‐derived lines with sequenced genomes of the Drosophila melanogaster Genetic Reference Panel (DGRP). We crossed the DGRP lines to P[GT1]‐element insertion mutants in Sema‐5c and neuralized (neur), two neurodevelopmental loci which affect olfactory behavior, and to their coisogenic wild‐type control. We observed significant variation in olfactory responses to benzaldehyde among F1 genotypes and for the DGRP line by mutant genotype interactions for both loci, showing extensive nonadditive genetic variation. We performed genome‐wide association analyses to identify the candidate modifier loci. None of these polymorphisms were in or near the focal genes; therefore, epistasis is the cause of the nonadditive genetic variance. Candidate genes could be placed in interaction networks. Several candidate modifiers are associated with neural development. Analyses of mutants of candidate epistatic partners with neur (merry‐go‐round (mgr), prospero (pros), CG10098, Alhambra (Alh) and CG12535) and Sema‐5c (CG42540 and bruchpilot (brp)) showed aberrant olfactory responses compared with coisogenic controls. Thus, integrating genome‐wide analyses of natural variants with mutations at defined genomic locations in a common coisogenic background can unmask specific epistatic modifiers of behavioral phenotypes.