Genetic Diversity Analysis of Indonesian Pigmented Rice Accessions Based on Functional Molecular Markers

Pigmented rice is functional staple food that becomes popular because of its anthocyanin content which is beneficial for health. Studies on the diversity of the local variety of Indonesian pigmented rice accessions have been carried out, but are still limited to one region of germplasm origin. This study aimed to analyze the genetic diversity of local varieties of pigmented rice collections of the IAARD-ICABIOGRAD Gene Bank. A total of 93 pigmented rice accessions from 16 provinces in Indonesia were analyzed using 15 functional molecular markers of SSR, STS, and indel. The total alleles detected were 115 with an average per locus of genetic diversity value of 0.71. There were five markers with PIC values >0.75, i.e. RM167, RM223, R8M33, R10M10, and GBSS1. The accessions were divided into two main groups based on their pericarp color. It is necessary to analyze the physicochemical content of the local rice accessions to complement the existing diversity information and identify potential pigmented rice accessions with high palatability.

Genomic Selection for F1 Hybrid Breeding in Strawberry (Fragaria × ananassa)

Cultivated strawberry is the most widely consumed fruit crop in the world, and therefore, many breeding programs are underway to improve its agronomic traits such as fruit quality. Strawberry cultivars were vegetatively propagated through runners and carried a high risk of infection with viruses and insects. To solve this problem, the development of F1 hybrid seeds has been proposed as an alternative breeding strategy in strawberry. In this study, we conducted a potential assessment of genomic selection (GS) in strawberry F1 hybrid breeding. A total of 105 inbred lines were developed as candidate parents of strawberry F1 hybrids. In addition, 275 parental combinations were randomly selected from the 105 inbred lines and crossed to develop test F1 hybrids for GS model training. These populations were phenotyped for petiole length, leaf area, Brix, fruit hardness, and pericarp color. Whole-genome shotgun sequencing of the 105 inbred lines detected 20,811 single nucleotide polymorphism sites that were provided for subsequent GS analyses. In a GS model construction, inclusion of dominant effects showed a slight advantage in GS accuracy. In the across population prediction analysis, GS models using the inbred lines showed predictability for the test F1 hybrids and vice versa, except for Brix. Finally, the GS models were used for phenotype prediction of 5,460 possible F1 hybrids from 105 inbred lines to select F1 hybrids with high fruit hardness or high pericarp color. These F1 hybrids were developed and phenotyped to evaluate the efficacy of the GS. As expected, F1 hybrids that were predicted to have high fruit hardness or high pericarp color expressed higher observed phenotypic values than the F1 hybrids that were selected for other objectives. Through the analyses in this study, we demonstrated that GS can be applied for strawberry F1 hybrid breeding.

Analysis of the inheritance of pericarp color and other characters in the rice hybrid Kuboyar × Gagat

Rice can form not only white, but also red, brown and black grains. In black rice, pericarp grains contain anthocyanins, which have antioxidant activity and are beneficial to human health. The purpose of the work is to study the inheritance of the black color of the pericarp and other qualitative traits in the intersubspecific hybrid of rice Kuboyar × Gagat, the selection of the best recombinant forms combining early ripeness, a compact erect panicle and black grain, the creation of the source material for practical selection. Methods The studies were carried out on hybrids of the first and second generation from crossing a white-grain variety of rice Kuboyar with black-grained Gagat in 2018–2019 in the Separate Division “Proletarskoye” of the Rostov Region. Results. A genetic analysis of the inheritance of the duration of the growing season, qualitative signs of coloring of flower scales and rice grains, and spinousness was carried out. In the second generation, 54 photosensitive non-flowering plants and 128 normal ones broke out, which indicates the interaction of four dominant genes in the genotype. The splitting according to the color of the pericarp was carried out according to the trihybrid scheme according to the type of com-plementarity in the ratio of 27 black: 21 brown: 16 white. The black color of the pericarp was formed when three dominant genes Kala1, 3, and 4 were present in the genotype, brown was determined by the Kala4 gene, and white by the remaining combinations of genes. According to the color of flowering scales, the cleavage occurred according to the digrid pattern: 9 black: 3 yellow with black apiculus: 4 straw yellow. Although the parental varieties were boneless, 39 spinous forms appeared in F2 with three complementary dominant genes An-a, An-b, An-c and inhibitor I, the remaining 89 plants were boneless. The best recombinant forms were selected, combining the optimal values of plants and panicles and black grain, the source material for practical selection was created.

Ectopic Expression of a Maize Gene Is Induced by Composite Insertions Generated Through Alternative Transposition

Transposable elements (TEs) are DNA sequences that can mobilize and proliferate throughout eukaryotic genomes. Previous studies have shown that in plant genomes, TEs can influence gene expression in various ways, such as inserting in introns or exons to alter transcript structure and content, and providing novel promoters and regulatory elements to generate new regulatory patterns. Furthermore, TEs can also regulate gene expression at the epigenetic level by modifying chromatin structure, changing DNA methylation status, and generating small RNAs. In this study, we demonstrated that Ac/fractured Ac (fAc) TEs are able to induce ectopic gene expression by duplicating and shuffling enhancer elements. Ac/fAc elements belong to the hAT family of class II TEs. They can undergo standard transposition events, which involve the two termini of a single transposon, or alternative transposition events that involve the termini of two different nearby elements. Our previous studies have shown that alternative transposition can generate various genome rearrangements such as deletions, duplications, inversions, translocations, and composite insertions (CIs). We identified >50 independent cases of CIs generated by Ac/fAc alternative transposition and analyzed 10 of them in detail. We show that these CIs induced ectopic expression of the maize pericarp color 2 (p2) gene, which encodes a Myb-related protein. All the CIs analyzed contain sequences including a transcriptional enhancer derived from the nearby p1 gene, suggesting that the CI-induced activation of p2 is affected by mobilization of the p1 enhancer. This is further supported by analysis of a mutant in which the CI is excised and p2 expression is lost. These results show that alternative transposition events are not only able to induce genome rearrangements, but also generate CIs that can control gene expression.

Inheritance of quantitative traits of the rice hybrid F2-F3 Svetly × Mavr

Rice can form not only white, but also red, brown and black kernels. In black rice, pericarp kernels contain anthocyanin, which has an antioxidant effect and is beneficial to human health. The current paper is devoted to the development of new rice lines with black pericarp based on the hybrid Svetly × Mavr. The purpose of the work is to develop new forms of rice with anthocyanin pericarp by a hybridization of varieties with white and black kernels, a genetic analysis of a number of quantitative traits and by a selection of the best variants with compact vertical black-kernel panicles to use them in future breeding work. There has been conducted a genetic analysis of varying quantitative traits affecting the rice productivity. The cleavage by a pericarp color was carried out according to the type of recessive epistasis in a ratio of 9 : 3 : 4. The black color of the pericarp was formed in the presence of two dominant genes Pb and Pp in the genotype, the brown color was due to the Pb gene, the white color was due to the rest combinations of genes. The traits “plant height” and “number of spikelets per panicle” of the hybrids F2 and F3 were inherited by the type of superdomination of large values of the trait controlled by two loci, the interaction of which resulted in transgressive forms. According to the traits “panicle length” and “1000 kernel weight”, there has been identified intermediate monogenic inheritance and two-peaked characteristic frequency distribution curves. There have been identified rice forms with black pericarp color, combining the optimal values of the traits “plant height”, increased “panicle length”, “number of spikelets per panicle” and “1000 kernel weight”. On its basis there has been also developed an initial material for practical breeding. The study was carried out in 2018–2020 on the fields of the EP “Proletarskoye” of the Rostov region.

Evaluation of Large-Sunflower Lines of Sunflower on Quantitative Morphological Traits

Confectionery sunflower - a special area of use of sunflower, which requires the creation of marketable seeds quality features. One of the possible ways to create large-fruited sunflower is to create production hybrids and lines. Objective: to evaluate the created new large-fruited sunflower lines by a complex of morphological characters and determine the best lines for use as large-seeds hybrids as parent components or source material. In 2016-2019 years on the basis of the Institute of Oilseed Crops NAAS a study was conducted to assess the economic characteristics of large-fruited sunflower lines. We studied a collection of 27 lines of large-seeds sources. The lines were created by direct selection or crossing and sampling: Reyny of Argentinean origin, Zaporizhzhya confectionery variety, confectionery hybrid with striped pericarp color of Israeli origin, white seed of Turkish origin, synthetic population - donor of complex resistance. To study from the collection, lines were drawn that went through at least 7 generations with selection for seed size. Experience has shown that the shortest growing season for lines 174d and KP11 was 99 days, and the longest for lines I2K670 was 109 days. In the studied collection, the greatest mass of 1000 seeds has the KP11-146.47g line, which is the mother component and does not have branching. The second by weight of 1000 seeds (109 g) stood out line 168v, which also had branches and pollen fertility restoration genes and will be used as the paternal form. The third largest is also one basket line ZKN51-100. The collection included lines originating from the same combination, but with a different morphotype for the presence and absence of branching. So, based on the combination of KP11 x Zaporizhzhya Confectionery, three lines were obtained. A mass of 1000 seeds was observed in 98-86 g, with the branching line having the largest mass of 1000 seeds. The lines created with one combination VK678 x ZKN32: with a branch 168a had a mass of 1000 seeds 95g, and a line 168b - without a branch 109 g. Of the two lines obtained from the descendants of the combination KP11 x the striped hybrid both had branches, but the seeds were much smaller (weight of 1000 seeds 59 and 79 g). The collection also studied samples created on the basis of varieties and populations 160c, 174, 175b, the mass of 1000 seeds of which turned out to be more acceptable for large-fruited use from 83 to 99 g. Summing up the results of studying the collection of newly created lines, we can highlight the lines 162d, 168v, 175b, KP11 that are potentially promising for use in hybrids. The selections showed that large-fruited lines can be obtained from large-fruited varieties, self-pollination of large-fruited hybrids and crossing lines with hybrids and varieties. Self-pollination and selection of large-fruited lines in several generations does not provide the necessary variability for positive changes in selections. The result of the selection by weight of 1000 seeds in the offspring from crosses and from populations creates opportunities for new large-seeds sunflower.

GENETICS OF THE TRAITS IN THE RICE HYBRID ‘SVETLY X MAVR

Rice can form not only white, but also red, brown and black kernels. In black rice pericarp contains anthocyanin pigment, which has antioxidant activity and is beneficial to human health. The article is devoted to the development of new rice lines with black pericarp on the basis of the hybrid ‘Svetly × Mavr’. The purpose of the work is to develop rice new lines with black seed vessel on the genetic background of the variety ‘Svetly’. There has been carried out a genetic analysis of varying quantitative traits that affect rice productivity. Cleavage by pericarp color occurred according to the dihybrid scheme according to the type of recessive epistasis in the ratio 9:3:4. The black color of the pericarp was formed with the presence of two dominant Pb and Pp genes in the genotype, the brown one was determined by the Pb gene, and the white one was determined by the other combinations of genes. Inheritance of plant height occurred according to the overdominance of large values of the trait. Parental forms differed in the allelic state of two pairs of genes. Along the panicle length, there has been determined partial negative dominance and monogenic differences of the hybridized varieties. According to ‘number of spikelets per panicle’, there has been identified an overdominance of a larger value of the trait and the interaction of two pairs of genes. According to ‘1000-kernel weight’, there has been established partial dominance of large values of the trait and monogenic differences of the initial parental forms. There have been selected the best recombinant forms combining a compact erect panicle and grains with a black seed vessel, and there has been developed starting material for practical breeding. The study was carried out on the fields of the Experimental Station “Proletarskaya” of the Rostov Region in 2018.

Tricin levels and expression of flavonoid biosynthetic genes in developing grains of purple and brown pericarp rice

The methylated flavone tricin has been associated with numerous health benefits, including reductions in intestinal and colon cancers in animal models. Tricin is found in a wide range of plant species and in many different tissues. However, whole cereal grains, such as rice, barley, oats, and wheat, are the only food sources of tricin, which is located in the bran portion of the grain. Variation in tricin levels was found in bran from rice genotypes with light brown, brown, red, and purple pericarp color, with the purple pericarp genotypes having the highest levels of tricin. Here, we analyzed tricin and tricin derivative levels in developing pericarp and embryo samples of a purple pericarp genotype, IAC600, that had high tricin and tricin derivative levels in the bran, and a light brown pericarp genotype, Cocodrie, that had no detectable tricin or tricin derivatives in the bran. Tricin and tricin derivatives were detected in both the pericarp and embryo of IAC600 but only in the embryo of Cocodrie. The purple pericarp rice had higher total levels of free tricin plus tricin derivatives than the light brown pericarp rice. When expressed on a per grain basis, most of the tricin component of IAC600 was in the pericarp. In contrast, Cocodrie had no detectable tricin in the pericarp samples but did have detectable chrysoeriol, a precursor of tricin, in the pericarp samples. We also used RNA-Seq analysis of developing pericarp and embryo samples of the two cultivars to compare the expression of genes involved in the flavonoid biosynthetic pathway. The results presented here suggest that understanding the basis of tricin accumulation in rice pericarp may lead to an approach to increasing tricin levels in whole grain rice. From analysis of gene expression levels in the pericarp samples it appears that regulation of the flavone specific genes is independent of regulation of the anthocyanin biosynthetic genes. It therefore may be feasible to develop brown pericarp rice cultivars that accumulate tricin in the pericarp.