Characterization of Functional Genes GS3 and GW2 and their Effect on the Grain Size of Various Landraces of Rice

Grain size is an essential factor in grain quality and yield. In the existing agricultural lands in Pakistan and even all over the world, genetics in rice works better for yield potential and quality improvement. GS3 and GW2 with functional mutation responsible for grain size in rice. In the current study, 17 different Pakistani landraces of various genetic and geographic backgrounds were evaluated for grain phenotypic traits (thousand-grain weight, length, width, and thickness) and characterized genotypes for GS3 gene (grain length) and GW2 (grain width). The two accessions JP5 and Bas370, were used as control. Phenotypic data revealed the range for grain weight from 16.86g (Lateefy) to 26.91g (PS2), grain length ranged from 7.27 mm (JP-5) to 12.18 mm (PS2), grain width ranged from 2.01 mm (Lateefy) to 3.51 mm (JP5), and grain thickness ranged from 1.79 mm to 2.19. Pearson correlation revealed a negative and significant correlation between grain width and length. There was no significant correlation between grain length and 1000-grain weight and grain width. LSD test displayed that the means of three variables grain length, grain width, and 1000-grain weight were statistically different from one another except grain width and grain breadth. GS3 is a negative regulator of grain length. Fifteen accessions GA-5015, PS-2, Swat-1, Swat-2, DR-2, Dilrosh, Malhar-346, Kashmir Basmati, Rachna Basmati, KS-282, Basmati-370, KSK-133, KSK-434, MG-Basmati, and Lateefy, carried the domesticated allele of GS3 while JP5 and Fakhr-e-Malakand carried the dominant allele. Similarly, the GW2 is a negative regulator of grain width. Fifteen accessions, i.e., Bas-370, GA-5015, PS-2, Swat-1, Swat-2, DR-2, Dilrosh, Malhar-346, Kashmir Basmati, Rachna Basmati, KS-282, KSK-133, KSK-434, MG-Basmati, and Lateefy carried the dominant allele while JP-5 and Fakhr-e-Malakand carried the mutant allele. The current phenotypic evaluation of the Germplasm revealed a diverse range of grain size of Pakistani landraces and also suggests that the selection of grain length in Pakistani landraces was independent of 1000-grain weight. The accessions with genotypic characterization will aid in marker-assisted breeding programs to break the stagnant yield prevail for the last few decades in Pakistan.

Inheritance of evolved thiocarbamate resistance in Rigid Ryegrass (Lolium rigidum) populations from Australia

Populations of rigid ryegrass (Lolium rigidum Gaudin) from southern Australia have evolved resistance to the thiocarbamate herbicide prosulfocarb. The inheritance of prosulfocarb resistance was explored by crossing R and S individuals. In all families within each cross, except 16.2, the response of the F1 were intermediate between the parents, suggesting that resistance is inherited as a single, partially dominant trait. For 16.2, the response of the F1 was more similar to the susceptible parent, suggesting resistance may be a recessive trait in this population. Segregation at the discriminating dose of 1200 g a.i. ha−1 prosulfocarb in populations 375-14 fitted the ratio (15:1) consistent with two independent dominant alleles; 198-15 fitted a ratio (13:3) for two independent alleles, one dominant and one recessive; and EP162 fitted a ratio (9:7) for two additive dominant alleles. In contrast segregation of population 16.2 fitted a (7:9) ratio consistent with two independent recessive alleles contributing to prosulfocarb resistance. Four different patterns of resistance to prosulfocarb were identified in different resistant populations, with inheritance as a dominant allele, dominant and recessive, additive dominant and as an independent recessive allele. This suggests there are several different mechanisms of prosulfocarb resistance present in L. rigidum.

New Simple Sequence Repeat Markers on Linkage Groups 2 and 7, and Investigation of New Sources of Eastern Filbert Blight Resistance in Hazelnut

Eastern filbert blight (EFB), caused by Anisogramma anomala, is a fungal disease threatening the european hazelnut (Corylus avellana) industry in the Willamette Valley of Oregon. The pathogen is endemic to the eastern United States where it causes little damage to the wild Corylus americana but causes severe cankers on most cultivars of the commercially important european hazelnut. The host genetic resistance in ‘Gasaway’ is conferred by a dominant allele at a single locus on linkage group 6 (LG6), and resistance from several other sources has been mapped to the same region. Some fungal isolates can overcome ‘Gasaway’ resistance, prompting a search for other sources of resistance. Resistance from other sources has been mapped to LG2 and LG7, for which additional simple sequence repeat (SSR) markers would facilitate marker-assisted selection (MAS). In this study, an in silico approach was used to develop new polymorphic SSR markers in the EFB resistance regions on LG2 and LG7. Starting with a search of 17 contigs of the ‘Jefferson’ genome sequence, 45 new polymorphic SSR markers were developed, characterized, and placed on the linkage map. The new SSR markers had an average of 10.18 alleles per locus, and average values for expected heterozygosity, observed heterozygosity, polymorphism information content, and frequency of null alleles of 0.72, 0.65, 0.68, and 0.068, respectively. Of the 42 new polymorphic SSRs segregating in the mapping population, 24 were on LG2, 12 were on LG7, and six were placed on other LGs. The new and previously developed SSR markers were used to study six new sources of EFB resistance, four from Russia and two from Crimea. Six resistant selections were crossed with susceptible selections, resulting in 7 progenies. Phenotyping for disease response revealed that segregation in progenies of the two Moscow selections (#2 and #27), one Russian selection (OSU 1187.101), and one Crimean selection (H3R12P62) fit the 1:1 segregation ratio expected for control of resistance by a dominant allele at a single locus; but in progenies of the other Russian selection (OSU 1166.123) and the other Crimean selection (H3R07P11), there was an excess of resistant seedlings. Correlation of disease scores and alleles at SSR loci indicated that resistance from three Russian selections (Moscow selections #2 and #27 and OSU 1166.123) and the Crimean selection H3R12P62 was on LG7, while resistance from Russian selection OSU 1187.101 was on LG2. Resistance from Crimean selection H3R07P11 was not correlated with markers on LG6, or LG2, or LG7. These sources and new SSR markers will be useful in MAS and the pyramiding of resistance genes in the breeding of new EFB-resistant cultivars.

A Dwarfing Gene sd1-d (Dee-geo-woo-gen dwarf) on Lodging Resistance and Related Traits in Rice

A dwarfing allele at the sd1 locus on chromosome 1 in rice, sd1-d, has been playing important role for developing lodging-resistant and high-yielding indica varieties IR8 and IR36. The dominant allele SD1 for long culm at the locus is differentiated into SD1-in and SD1-ja that are harbored in indica and japonica subspecies, respectively. The sd1-d of IR36 was substituted with SD1-in or SD1-ja by 17 backcrosses with IR36, and two isogenic tall lines were developed by using an indica variety IR5867 and a japonica one ‘Koshihikari’ as donors, which were denoted by “5867-36” and “Koshi-36’’, respectively. The present study was conducted to examine the effect of dwarfing gene sd1-d on lodging resistance and related traits, compared with SD1-in and SD1-ja. Two isogenic lines and IR36 were cultivated in the field of the Faculty of Agriculture and Marine Science, Kochi University, Japan during 2017. Regarding index of lodging (g·cm/g × 100), genotypes were in the order: 5867-36 (97.4) > Koshi-36 (74.1) > IR36 (46.0) on the 21st-day after 80%-heading, and they were in the same order on 10th-day after 80%-heading. The 4th-panicle length (cm) was in the order: 5867-36 (118.7) > Koshi-36 (97.6) > IR36 (78.6). Similarly, the 4th-top weight (g) was in the order: 5867-36 (12.2) > Koshi-36 (10.2) > IR36 (9.6). The highest breaking strength (g) was recorded in IR36 (1649) followed by 5867-36 (1493) whereas the lowest breaking strength (g) was recorded in Koshi-36 (1360). Consequently, it is inferred that sd1-d enhances lodging resistance due to the decreases in the length and weight above the 4th-internode as well as the increase of breaking strength. The effect of SD1-in on lodging resistance is lower than that of SD1-ja.

The molecular basis for allelic differences suggests Restorer-of-fertility 1 is a complex locus in sugar beet (Beta vulgaris L.)

Background Cytoplasmic male sterility (CMS) is a widely used trait for hybrid seed production in many crops. Sugar beet CMS is associated with a unique mitochondrial protein named preSATP6 that forms a 250-kDa complex. Restorer-of-fertility 1 (Rf1) is a nuclear gene that suppresses CMS and is, hence, one of the targets of sugar beet breeding. Rf1 has dominant, semi-dominant and recessive alleles, suggesting that it may be a multi-allelic locus; however, the molecular basis for differences in genetic action is obscure. Molecular cloning of Rf1 revealed a gene (orf20) whose protein products produced in transgenics can bind with preSATP6 to generate a novel 200-kDa complex. The complex is also detected in fertility-restored anthers concomitant with a decrease in the amount of the 250-kDa complex. Molecular diversity of the Rf1 locus involves organizational diversity of a gene cluster composed of orf20-like genes (RF-Oma1s). We examined the possibility that members of the clustered RF-Oma1 in this locus could be associated with fertility restoration. Results Six yet uncharacterized RF-Oma1s from dominant and recessive alleles were examined to determine whether they could generate the 200-kDa complex. Analyses of transgenic calli revealed that three RF-Oma1s from a dominant allele could generate the 200-kDa complex, suggesting that clustered RF-Oma1s in the dominant allele can participate in fertility restoration. None of the three copies from two recessive alleles was 200-kDa generative. The absence of this ability was confirmed by analyzing mitochondrial complexes in anthers of plants having these recessive alleles. Together with our previous data, we designed a set of PCR primers specific to the 200-kDa generative RF-Oma1s. The amount of mRNA measured by this primer set inversely correlated with the amount of the 250-kDa complex in anthers and positively correlated with the strength of the Rf1 alleles. Conclusions Fertility restoration by sugar beet Rf1 can involve multiple RF-Oma1s clustered in the locus, implying that stacking 200-kDa generative copies in the locus strengthens the efficacy, whereas the absence of 200-kDa generative copies in the locus makes the allele recessive irrespective of the copy number. We propose that sugar beet Rf1 is a complex locus.

STUDY OF GENETIC DIVERSITY USING MICROSATELLITE MARKERS IN IRAQI SHEEP BREEDS

Genotypes and allele frequency values ​​were studied to determine the genetic diversity of three microsatellite markers (BM1329, BM134 and CSSM66) in two local Iraqi sheep breeds (50 Awasi ewes (AW) and 50 Naimi ewes (NA)) and breed in one Agricultural Stations in middle of Al-Furut Iraq (Karbala Governorate). The Genetic analyses for the study were carried out at the Biotechnology Research Center / Al-Nahrain University using PCR technology to obtain alleles for the studied microsatellites. The results of this study indicate that there is a multiplicity of genotypes and alleles resulting from these markers among the members of the single breed and between the studied breeds. It was revealed that the allele frequency values showed the presence of alleles dominant on the rest of alleles produce in this sample studied, the BM1329 microsatellite of the Awassi breed produced the dominant allele frequency in 195(0.25) and 320 (0.25), While in the Naimi breed were the values ​​of the dominant allele frequency of the195(0.22), 220(0.21) and 230(0.24), and the dominant allelic frequency of (BM134) marker in the Awassi breed was 118 and 135 and repeated (0.21 and 0.26, respectively). For CSSM66 microsatellite, the dominant allelic results and their allelic frequency values ​​were (195 (0.20), 205 (0.23) and 220 (0.25)) for Awasi breed, whereas it was 180 (0.24), 195 (0.28) and 220 (0.22) for Nuaimi breed. These results enable us to use these markers as a means of determining the diversity and genetic relationships between individuals of a single breed as well as between breeds.

Identification of spring wheat lines by the allelic state of Vrn genes for use in winter wheat breeding for carotenoid content

The aim of the research is allelic identifi cation of the genes Vrn A1, Vrn B1, Vrn B3, and Vrn D1 in 18 spring wheat samples and 3 lines obtained from winter-spring cross combinations with high carotenoid grain content for winter wheat breeding program. The content of carotenoid pigments in the grain ranged from 0.20 to 8.3 mg/100 g in the analyzed 143 samples of soft wheat. Samples of spring wheat were identifi ed for high content of carotenoids (more than 4.5 mg/100 g of flour): Volgouralskaya, Kinelskaya 61, Lutescens 540, Lutescens 598, Lutescens 575, Lutescens 516, Kinelskaya 2010, Omskaya 41. According to the studies, the presence of the Vrn-A1 allele established in 4 spring wheat samples (Sibiryachka 4, Frontana, Izolda, Dynastiya). The heterozygous state of the Vrn-A1 gene was determined for the Saratovskaya Zolotistaya variety. The presence of the allele Vrn-B1 was identifi ed in the samples Fora, Leningradka, Izolda, Saratovskaya Zolotistaya, Omskiy Tsirkon, Omskaya 41, Lutescens 540. For the samples Lutescens 516, L224-5 the heterozygous state of the locus Vrn-B1was determined. Analysis of the Vrn-B3 gene confi rmed the presence of the Vrn-B3 allele in all tested samples. Only variety Dynastiya carried a dominant allele. The Vrn-D1 gene was identifi ed in a recessive state in samples Fora, Sibiryachka 4, Novosibirskaya 22, Frontana, Leningradka, Kinelskaya 2010, Kinelskaya 61, Volgouralskaya, Omskaya 41, Lutescens 516, Lutescens 540, Lutescens 598, L224–5. In the variety Omskiy Tsircon gene Vrn-D1 was in a heterozygous state. The use of spring carriers of the trait – Samples Omskaya 41 and Lutescens 540, with one dominant gene Vrn-A1, and Lutescens 516, with the dominant allele of the gene Vrn-A1 and polymorphic in the Vrn B1 gene – were the most promising for the winter wheat breeding in the direction of increasing the carotenoids content in flour. Key words: bread wheat, variety, line, vernalization, carotenoids, genes Vrn A1, Vrn B1, Vrn B3, Vrn D1.

Modeling Y-Linked Pedigrees through Branching Processes

A multidimensional two-sex branching process is introduced to model the evolution of a pedigree originating from the mutation of an allele of a Y-linked gene in a monogamous population. The study of the extinction of the mutant allele and the analysis of the dominant allele in the pedigree is addressed on the basis of the classical theory of multi-type branching processes. The asymptotic behavior of the number of couples of different types in the pedigree is also derived. Finally, using the estimates of the mean growth rates of the allele and its mutation provided by a Gibbs sampler, a real Y-linked pedigree associated with hearing loss is analyzed, concluding that this mutation will persist in the population although without dominating the pedigree.

Identification of allelic combinations of the Ppd-D1, Vrn-A1, Vrn-B1 and Vrn-D1 genes in common wheat lines obtained in the National Center of Grain named after P. P. Lukyanenko

An analysis of the allelic composition of the genes determining photoperiodic sensitivity (Ppd-D1) and the need for vernalization (Vrn-A1, Vrn-B1, Vrn-D1) was carried out in 286 common wheat lines obtained in the National Center of Grain named after P. P. Lukyanenko with the use of allele-specific primers. The analyzed samples were distributed over 21 haplotypes; the dominant allele of the Ppd-D1a gene prevailed in the studied material. 123 lines of common wheat carry a combination of D-RRD alleles. The lines that can be attributed to the group of alternate wheat (R-RDR, R-RRD) were identified. All studied samples carry the recessive allele of at least one VRN1 gene.

Inheritance of Top Branching in Sunflower (Helianthus Annuus L.) Collection Samples

Aim of our research was to study the genetic diversity and establish the inheritance of top branching trait in the collection of 34 sunflower lines of the Institute of Oilseed Crops of the NAAS. Experiments were carried out in 2005–2016 according to classical cultivation methods, using manual castration, crossings, forced self-pollinating, isolation and visual assessment of the first and second generation of obtained descendants. The statistical reliability of the obtained ratio was confirmed by calculating the Pearson’s chi-squared test. Presence of two loci determining the inheritance of the branching trait in sunflower was established. In one locus, recessive alleles are responsible for manifestation of the branching trait. In the second locus, dominant alleles are responsible for the manifestation of the branching trait. In 23 lines of sunflower, it was established that a recessive homozygote for one gene causes phenotypical top and full branching. In 8 lines of the collection, full branching trait is due to the dominant allele of the gene. In the lines InK235, APS49, the presence of two genes was established, the dominant alleles of which determine full branching trait. In the APS56 line, full branching is controlled by the dominant alleles of three genes.