Introgression Of Desirable Traits Research Articles

Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae.

Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.

Introgression of desirable traits from Cicer reticulatum into cultivated chickpea (Cicer arietinum L.)

Introgression of desirable traits from Cicer reticulatum into cultivated chickpea (Cicer arietinum L.)

Biodiversity of interspecific hybrids of the genus <i>Allium</i> L.

Relevance. Interspecific hybridization in the genus Allium L. is the best way to increase biodiversity by introgression of desired traits within the genus. This is valuable for signs such as resistance to diseases and pests, accumulation of important metabolites, obtaining new sources of cytoplasmic male sterility. The creation based on interspecific hybridization of fundamentally new plant forms with unique genetic material makes it possible to expand the selection of genotypes that are valuable in practical terms.Methods. To characterize the breeding material, the plants of interspecific allium hybrids were evaluated using morphological and phytopathological analyses. The analysis of plants of interspecific hybrids of the genus Allium L. from various inbred offspring from BC1-2 combinations of crossing species A. cepa × A. vavilovii and A. cepa × A. fistulosum by breeding characteristics was carried out. Plants were studied by weight, color, bulb shape, number, height of seed stalks, seed productivity and resistance to downy mildew.Results. The biodiversity of plants was revealed: by weight, shape, color of the bulb; by resistance to downy mildew of plants of the first year of vegetation and seed plants; by the number, height of seed stalk; by seed productivity. Plants of interspecific allium hybrids formed bulbs weighing up to 120 g, white, yellow, brown and red, elliptical, broadly elliptical, round and transversely elliptical bulb shape. Phytopathological assessment of allium plants of the first year of vegetation and seed plants revealed diversity in inbred offspring with resistance to peronosporosis. In the combination of crossing species A. cepa × A. vavilovii plants of the first year of vegetation had the largest number of resistant plants to downy mildew (up to 66.7%). According to the seed productivity of plants, depending on the combination of crossing, inbreeding generation and backcross, highly fertile plants with increased seed setability (up to 2.0 g /plant) were identified. The conducted studies have demonstrated an increase in the biodiversity of allium plants obtained based on interspecific hybridization, backcrosses and inbreeding.

The genome sequencing and comparative analysis of a wild kiwifruit Actinidia eriantha

The current kiwifruit industry is mainly based on the cultivars derived from the species Actinidia chinensis (Ac) which may bring risks such as canker disease. Introgression of desired traits from wild relatives is an important method for improving kiwifruit cultivars. Actinidia eriantha (Ae) is a particularly important taxon used for hybridization or introgressive breeding of new kiwifruit cultivars because of its valued species-specific traits. Here, we assembled a chromosome-scale high-quality genome of a Ae sample which was directly collected from its wild populations. Our analysis revealed that 41.3% of the genome consists of repetitive elements, comparable to the percentage in Ac and Ae cultivar “White” genomes. The genomic structural variation, including the presence/absence-variation (PAV) of genes, is distinct between Ae and Ac, despite both sharing the same two kiwifruit-specific whole genome duplication (WGD) events. This suggests that a post-WGD divergence mechanism occurred during their evolution. We further investigated genes involved in ascorbic acid biosynthesis and disease-resistance of Ae, and we found introgressive genome could contribute to the complex relationship between Ae and other representative kiwifruit taxa. Collectively, the Ae genome offers valuable genetic resource to accelerate kiwifruit breeding applications.

ValSten: a new wild species derived allotetraploid for increasing genetic diversity of the peanut crop (Arachis hypogaea L.)

Introgression of desirable traits from wild relatives plays an important role in crop improvement, as wild species have important characters such as high resistance to pests and pathogens. However, use of wild peanut relatives is challenging because almost all wild species are diploid and sexually incompatible with cultivated peanut, which is tetraploid (AABB genome type; 2n = 4x = 40). To overcome the ploidy barrier, we used 2 wild species to make a tetraploid with the same allotetraploid genome composition as cultivated peanut. Crosses were made between 2 diploid wild species, Arachis valida Krapov. and W.C. Greg. (BB genome; 2n = 2x = 20) and Arachis stenosperma Krapov. and W.C. Greg. (AA genome; 2n = 2x = 20). Cuttings from the diploid F1 AB hybrid were treated with colchicine to induce chromosome doubling thus generating an induced allotetraploid. Chromosome counts confirmed polyploidy (AABB genome; 2n = 4x = 40). We named the new allotetraploid ValSten. Plants had well-developed fertile pollen, produced abundant seed and were sexually compatible with cultivated peanut. ValSten exhibits the same high resistance to early and late leaf spot and rust as its diploid parents. Notably, we observed morphological variations, including flower width and branch angles in the earliest generation (S0) of allotetraploids. A SNP array was used to genotype 47 S0 allotetraploids. The great majority of markers showed the additive allelic state from both parents (AABB). However, some loci were AAAA or BBBB, indicating homeologous recombination. ValSten provides a new, vigorous, highly fertile, disease resistant germplasm for peanut research and improvement.

Review on Somatic Hybridization and Its Role in Crop Improvement

Somatic hybridization is one of the most important uses of protoplast culture. This is particularly significant for hybridization between species or genera, which cannot be made to cross by conventional methods of sexual hybridization. The aim of somatic hybridization is to transfer traits which are desired and generate a beneficial crop plants without genetic engineering and as well as facilitate conventional breeding through providing novel crop lines. Somatic hybridization broadens the base of accessible germplasm and offers additional opportunities for introgression of desirable traits into cultivars. Plant protoplasts can be fused and the fusion products cultured to produce somatic hybrid plants. This technique has been used to produce germplasm previously unavailable to the plant breeder. Several researchers have emphasized production of hybrids between distantly related, sexually incompatible species, but many of these hybrids are sterile, precluding incorporation into a breeding program. Hence, to transfer traits such as disease and herbicide resistance, emphasis has shifted to production of hybrids between more closely related species. Novel variation has been observed in such somatic hybrids due to segregation of mixed organelles, cytoplasmic and nuclear gene recombination, and somaclonal variation. The unique gene combinations made possible by protoplast fusion ensure that new plant varieties will soon be derived from somatic hybridization. Even though measurable success of somatic hybridization in terms of cultivar release may still be limited, the potential for their use in plant breeding remains great. In general, somatic hybridization provides excellent opportunities for research on plant improvement, first by exploring genetic variations among the existing crops and then by attempting to transfer the available genetic information from one species to another through fusion of protoplasts isolated from somatic tissues of these crops. Somatic hybridization is contributing to plant breeding in overcoming common crossing barriers among plant species. Some of the problems could be overcome by somatic hybridization are: sexual incompatibility, nucellar embryogenesis, male or female sterility, transfer of resistance genes for biotic and abiotic stresses, to create novel hybrids with increased yields. Several steps are involved in the somatic hybridization process. Some of them are: identification of the source of protoplasts, isolation of protoplasts, planting of protoplasts, regeneration of plants, fusion of protoplasts, selection procedures, identification and characterization of somatic hybrid plants. Generally somatic hybridization is playing a key role in the production of novel interspecific and intergeneric hybrids and transfer of genes for diseases resistance, abiotic stress resistance, herbicide resistance and many other quality characters. Besides being of value for the transfer of unidentified genes, somatic hybridization is a tool for the modification and improvement of polygenic traits. Furthermore, the modification of organellar genetic material is possible via somatic hybridization since a mixture of the two fusion partners is obtained in the hybrid cell Production of hybrid plants through the fusion of protoplasts of two different plant species/varieties. Keywords: Somatic; Hybridization; Protoplast; Fusion. DOI: 10.7176/JBAH/10-11-04 Publication date: June 30 th 2020

Development of intron length polymorphic (ILP) markers in onion (Allium cepa L.), and their cross-species transferability in garlic (A. sativum L.) and wild relatives

Onion (Allium cepa L.) is a popular spice and a plant of high medicinal value. Conventional breeding and genetic improvement efforts were largely limited due to self-incompatibility and heterozygosity. Recently, marker assisted breeding has significantly reduced time and labour in developing elite varieties. But very limited polymorphic and cross-transferable markers are available in onion. There is an urgent need to develop polymorphic markers in Allium to expedite and introgress desirable traits from wild relatives (which are rich bioresource of various biotic and abiotic resistance genes) to A. cepa. Considering limited availability of reliable molecular markers in Allium and wild relatives, in current study, 20,204 ESTs (3750 contigs and 8364 singletons), of A. cepa were successfully utilized for identification of over 2689 intron length polymorphic (ILP) markers. A set of 30 markers was tested for polymorphism in onion and cross-transferability in garlic and related wild species. Among these, eighteen markers amplified at least one of the accessions of A. cepa. Transferability of these ILP markers was ranged from 21.7 to 95.7% in Allium spp. Low level of polymorphism in A. cepa compared to wild Allium species is reported. Based on the Jaccard dissimilarity matrix, a neighbour-joining tree was constructed, which clustered all the 23 varieties/accessions under three groups. All the varieties of A. cepa were clearly clustered separately under group I. However, there was intermixing of varieties/accessions of A. sativum L. and wild relatives, which may possibly be due to less number of markers validated for cross-transferability. In future, larger set of markers will be used to resolve the genetic variations among wild varieties and A. sativum These 18 polymorphic ILP markers could be utilised for diversity characterization of Allium spp., varietal identification, mapping of genes and introgression of desirable traits from wild relatives.

Diversity and conservation priorities of crop wild relatives in Mexico

AbstractCrop wild relatives (CWR) are valuable resources for crop breeding due to their close genetic relationship to the cultivated plants and their wide genetic variation, allowing the introgression of desirable traits into the crops, such as resistance to plant pests and diseases or adaptability to climate change. Mexico is a centre of agrobiodiversity, including CWR, but climate change, and other factors, are contributing to the loss of important Mexican CWR genetic diversity. Thein situandex situconservation status of Mexican priority CWR were assessed through a gap analysis as part of a national CWR conservation strategy for Mexico, to ensure the long-term preservation and improve the availability of these genetic resources. A set of 310 priority CWR taxa, previously identified as part of the national CWR inventory for Mexico, were analysed. Species distribution modelling and ecogeographic diversity analyses were used to detect gaps inin situandex situconservation at taxon and ecogeographic levels. Priority target sites were identified throughout the country for complementaryin situandex situconservation of these taxa. The results obtained allow us to make recommendations for immediate conservation actions, thus helping to mitigate the threats to Mexican agrobiodiversity and enhance both national and global food security.

QTL analysis on rice genotypes adapted to acid sulfate soils in the Mekong river delta, Vietnam

Three target points in acid sulfate soils have been identified as: 1) Aluminum (Al) toxicity; 2) Iron (Fe) toxicity; 3) Phosphorous (P)deficiency; and 4) Droughts at the seedling stage. The exploitation of gene pools from wild rice species fruitfully obtained a true introgression of desirable traits into high yielding varieties (HYVs), such as AS996 (IR64/Oryza rufipogon), which are tolerant to Al-toxicity, have short durations, high yields, and adaptability to acid sulfate soils. Major QTLs on chromosome 3 were detected to control Al-toxicity as identified through an analysis of the RIL population of IR64/O. rufipogon on control relative root length (RRL). RM232 was considered as a good marker linked to the target quantitative trait locus(QTL)on chromosome 3, then SR28 and OSR29 on chromosome 9 were also used.QTL mapping by 126 SSRs through 225 individuals of the F6 RILs population of AS996/OM2395 was carried out to find the P-uptake gene on chromosome 12. The promising genotype of OM4498 from the BC population of IR64/OMCS2000 was selected through MAS with RM235 and RM247 on chromosome 12 linked to QTL, which controls the P-deficiency tolerance. Based on the leaf bronzing index (LBI), SSR markers were used to select promising genotypes tolerant to iron-toxicity, such as RM315 and RM212 on chromosome 1, and RM252 and RM211 on chromosome 2. The intervals among RM315-RM212 on chromosome 1, RM6-RM240 on chromosome 2, and RM252-RM451 on chromosome 4, were continually studied through further fine mapping.A backcrossing mapping population that included 217 individuals of BC2F2, was set up from OM1490/WAB880-1-38-18-20-P1-HB to detect the QTLs relating to drought tolerance (DT). The QTL was located in the intervals between RM201-RM511 on chromosome 9. BAC clones 13A9 and 7O3 were used as pinpoints on the high solution map for new markers designed from their sequences. The markers became useful to help rice breeders possibly select the improved genotypes adapting to drought stress in the seedling stage.

OMICS based Interventions for Climate Proof Crops

Agriculture – the key to human civilization without doubt can be regarded as an essential part of our daily lives providing us our bread and butter. Food production or creation of fibers, fuels, raw materials & biopharmaceuticals forming the fundamental basis of human and animal sustenance is because of crop and other plant species. With a long history of humankind and agriculture co-existence, and immense & indispensable importance of agriculture in human sustenance today, it is therefore our duty to further promote and sustain agriculture. The present global scenario takes our attention to what we call ‘Climate Change’. Adverse change in climate can lead to imbalance in food production and ultimately imbalance of the human health, nutrition, and happiness. It is evident that the impact of climate change covers all regions. Thus, we need strategies that enable us to increase our food production to feed the ever-growing human population and at the same time keep sustainability and effect on environment in mind. This is where the term sustainable agriculture comes into play. Indefinite food production without causing severe or irreversible damage to the ecosystem is the key. Sustainable agriculture should not be misunderstood by totally abolishing new technologies. But it actually aims at developing technologies that helps in improving agriculture production without having negative impact on the environment. We here propose certain biotechnology-based strategies that can overcome negative impact of climate change and will also lead in improving future food production and livelihood. Droughts, irregular precipitations, deviated temperatures are predicted to be frequent in the near future. The question is, how do we tackle these problems? There is a need to have climate proof crops, i.e. the crops that can sustain various abiotic stresses. So far conventional means have been exploited but looking at the looming population and the intensity of climatic vagaries the need is to focus on new technologies having solutions with sustainability. One such technology is omics, and where transcriptomics and proteomics are two key approaches. Large numbers of genes/proteins that are involved in regulating different stresses and finally can be exploited to generate next-generation crops to enable enhanced food production are available. Molecular breeding has tremendous scope that will ensure introgression of desirable traits in cultivars without any linkage drag. Biotechnology also provides us the platform to look for desirable genes across genera and even the kingdom. Thus genome revolution has to play a role in next green revolution to have climate proof crops that can improve future food production and livelihood for sustainable human habitations.

Establishment of Molecular Linkage Maps Using SRAP Markers in Sweet Potato

Sweet potato [Ipomoea batatas(L.) Lam.] is an important vegetative reproduction crop.Despite its worldwide importance,molecular biology researches in sweet potato have lagged behind other crops due to its characteristics including polyploidy,outcrossing behavior,and high heterozygosity.As a result,it is difficult to make a breakthrough for the improvement of sweet potato using conventional methods.In this study,sequence-related amplified polymorphism(SRAP) markers were applied to establish molecular genetic linkage maps with F1 population consisting of 240 individuals derived from a cross of sweet potato cv.Luoxushu 8(high starch content cultivar)×cv.Zhengshu 20(low starch content cultivar).A total of 770 and 523 SRAP markers were generated,respectively,in Luoxushu 8 and Zhengshu 20.Using the software of JoinMap 3.0 and the 'double pseudo testcross strategy',a molecular linkage map containing 81 linkage groups was established with 473 SRAP markers in Luoxushu 8,and the map covered 5 802.46 cM with an average marker interval of 10.16 cM.In Zhengshu 20,the molecular linkage map containing 66 linkage groups was constructed using 328 SRAP markers,and the map covered 3 967.90 cM with an average marker interval of 12.02 cM.These results will provide a powerful tool to facilitate the introgression of desired traits into cultivars,gene localization,and map-based cloning techniques,and greatly increase breeding efficiency through marker-assisted selection(MAS) techniques.

Variation in Anther Culture Response and Fertility of Backcrossed Hybrids between Indica and Japonica Rice (Oryza sativa)

This study was conducted to investigate the variations of fertility, callus induction and plant regeneration in backcrossed hybrids between a responsive japonica variety (Mankeumbyeo, recurrent parent) and a recalcitrant indica variety (Ranta Emas, donor parent) to anther culture. The mean spikelet fertility of inter-subspecific F1 and BC1F1 hybrids was 33.5% and 67.2%, and the spikelet fertility of BC1F1 among backcrossed hybrids showed the most extensive variation (a low of 4.5% to a high of 90.6%). The mean fertility and distribution range in BC5F1 hybrids were almost the same as that of the japonica recurrent parent (94.6%). The mean callus induction of F1 and BC1F1 hybrids was higher than that of donor parent, and the distribution range in BC1F1 hybrids varied from a low 0% to a high 18.7%. The mean callus induction and plant regeneration of BC4F1 hybrids was almost that of japonica recurrent parent, and there were no statistical differences between BC4F1 and BC5F1 hybrids. These results may help to accelerate the introgression of desirable traits from indica into japonica rice using anther culture of backcross hybrids as a breeding strategy.

Cytogenetic analysis of interspecific hybrids in genus Citrullus (Cucurbitaceae)

Investigations on interspecific crossability in two species of the genus Citrullus were studied based on their morphology, chromosome pairing and pollen fertility in their hybrids resulting from 12 combinations(including reciprocals). These have been utilized for tracing the phylogenetic relationship between the taxa and factors responsible for their differentiation. A collective evaluation of data on cross compatibility,morphology, chromosome association and pollen fertility indicated a close phylogenetic relationship between the species C. colocynthis (wild2n = 22) and C. vulgaris (cultivated 2n = 22). Significant differences for crossability and pollen fertility were observed between hybrids of C. colocynthis × C. vulgaris and reciprocals. Meiotic analysis of F1 hybrids revealed that these two species are freely crossable and provide normal chromosome association, involving an average of 9 to maximum 11 pairs of chromosomes. This indicated the possibility of high recombination and thereby genetic introgression of desirable traits. As both the species are of economic significance, breeding strategies can be developed for the genetic improvement of these species.

Insect-resistant plants with improved horticultural traits from interspecific potato hybrids grown in vitro

Plants were regenerated from petiole calli of interspecific hybrids of Solanum tuberosum x S. berthaultii, an insect-resistant wild species. Callus culture was used to generate genetic changes to overcome the restricted recombination between the two genomes. Two plants out of 58 (3.5%) from calli of hybrid J114-1 showed stable and heritable differences from the hybrid over two cycles of evaluations in the field. Replicated trials were conducted in 1987 and 1988, using two populations of plants propagated by nodal cuttings from the original regenerates maintained in vitro. One regenerate showed insect resistance and increased marketable yield (approximately two fold) in the field. The other had higher levels of phenolic exudate in one of the two types of foliar trichomes associated with the insect resistance mechanism. Some desirable changes were discernible only in sexual progeny of regenerates, not in the regenerates themselves. In a backcross to S. tuberosum, 7 of 14 (50%) regenerates from hybrid F743-4 showed more progeny (up to 15-fold) with improved trichome traits and horticultural characteristics than the original hybrid. The variations were not associated with changes in ploidy. Fifteen plants obtained from these crosses are currently being incorporated into breeding lines. These results suggest that a period of callus culture followed by plant regeneration may aid in the introgression of desirable traits from wild species into crop plants.