Pre-breeding Programs Research Articles

Importance of Potato as a Crop and Practical Approaches to Potato Breeding.

Potatoes (Solanum tuberosum L. subsp. tuberosum and andigena) and seven other related species, which are cultivated today, have become the most important non-cereal crop in the world. It is grown on a significant scale in 130 countries, with a gross production value of 63.6 billion US dollars in 2016, with the yearly potato production of 368 million tons in 2018. Today potato is grown for food, animal feed, industrial uses, and seed tuber production, depending on the region, country development, and historical reasons. The food production is both for fresh ware markets and for processing into crisps, french fries, canned potatoes, flakes, etc. More than 10,000 potato varieties have been grown worldwide to date, many of which are still grown. Despite such a large number of varieties, there is still a need for new varieties. Classical breeding of new potato varieties in many programs around the world has changed little in decades and differs mainly in terms of scope and technologies used. Until the turn of the millennium, it was based primarily on empirical experience and selection of individual phenotypic traits. The great genetic diversity that exists in potato and its wild relatives is both an opportunity and a challenge to introduce traits that do not currently exist in the potato gene pool into modern potato varieties. Molecular marker technology development has reached the point where published markers for use in commercial breeding are available. Markers can be used during the whole selection process, with an even more important role of molecular breeding in pre-breeding programs and creation of the most appropriate parental lines.

Lessons from a GWAS study of a wheat pre-breeding program: pyramiding resistance alleles to Fusarium crown rot

Much has been published on QTL detection for complex traits using bi-parental and multi-parental crosses (linkage analysis) or diversity panels (GWAS studies). While successful for detection, transferability of results to real applications has proven more difficult. Here, we combined a QTL detection approach using a pre-breeding populations which utilized intensive phenotypic selection for the target trait across multiple plant generations, combined with rapid generation turnover (i.e. “speed breeding”) to allow cycling of multiple plant generations each year. The reasoning is that QTL mapping information would complement the selection process by identifying the genome regions under selection within the relevant germplasm. Questions to answer were the location of the genomic regions determining response to selection and the origin of the favourable alleles within the pedigree. We used data from a pre-breeding program that aimed at pyramiding different resistance sources to Fusarium crown rot into elite (but susceptible) wheat backgrounds. The population resulted from a complex backcrossing scheme involving multiple resistance donors and multiple elite backgrounds, akin to a MAGIC population (985 genotypes in total, with founders, and two major offspring layers within the pedigree). A significant increase in the resistance level was observed (i.e. a positive response to selection) after the selection process, and 17 regions significantly associated with that response were identified using a GWAS approach. Those regions included known QTL as well as potentially novel regions contributing resistance to Fusarium crown rot. In addition, we were able to trace back the sources of the favourable alleles for each QTL. We demonstrate that QTL detection using breeding populations under selection for the target trait can identify QTL controlling the target trait and that the frequency of the favourable alleles was increased as a response to selection, thereby validating the QTL detected. This is a valuable opportunistic approach that can provide QTL information that is more easily transferred to breeding applications.

Harnessing wild relatives of pearl millet for germplasm enhancement: Challenges and opportunities

AbstractPearl millet [Pennisetum glaucum (L.) R. Br.] is one of the world's hardiest warm‐season cereal crop and is cultivated mainly in the semi‐arid tropics of Asia and Africa for food, feed, fodder, and brewing. It is mainly cultivated for its gluten‐free grains with high content and better quality of nutrients. Pearl millet is a resilient crop that can produce grain and biomass under harsh conditions like low fertility, erratic rainfall, acidic and saline soils, and the hottest climates. However, biotic stresses such as downy mildew and blast diseases and abiotic stresses, especially drought and seedling‐ and flowering‐stage heat stress, pose constant threat to the realization of yield potential of this crop. To make further improvement in threshold level of abiotic and biotic stress tolerance, breeders are looking for novel genes in diverse germplasm sources. Crop wild relatives (CWRs) could be a source of novel genes that are important for diversification of the genetic base of pearl millet. A stage‐gate process is proposed for the efficient management of prebreeding programs using CWRs as a source of germplasm diversity and improvement. This article explains the various strategies for capturing and using alleles for climate resilience traits improvement. This article covers breeders’ perspectives on importance of using CWRs as germplasm source for crop improvement. This article also describes the availability of CWRs, characterization of new traits and the strategies to be applied for the identification and introduction of genes of interest in elite breeding lines and commercial varieties and hybrids of pearl millet.

Use of plant genetic resources in crop improvement–example of Serbia

Plant genetic resources are a link between agriculture, environment and trade, so their conservation requires cooperation from different sectors. The existing diversity in genetic resources is the foundation in breeding for new challenges or new markets in the future. The number of crop genetic resources in Serbia is obscure because there is no national inventory. It is thought that there are about 15,000 seed accessions and 3500 accessions of fruit trees and grape in collections of different national institutes and stakeholders. In the National Plant Gene Bank, there are more than 4000 accessions of nearly 250 plant species. Crops kept in ex situ collections are used in breeding programs and interspecific crosses, for selection and introduction of desired traits through pre-breeding programs. Serbia as a state participates in all national and international efforts for preservation, management and use of plant genetic resources. Additionally, Serbia has also established a set of national regulations related to plant genetic resources and their use in breeding. Since Serbia is one of Europe’s most important crop producers, especially in maize (11% of EU-27 production), soya (35%), sunflowers (6%) and sugar beet (2.5%), this paper discusses certain issues and achievements in the use of plant genetic resources in cereal and oil crops improvement in Serbia, as well as national and international regulations affecting their exploitation.

Genomic assessment of white clover and perennial ryegrass genetic resources

Forage resources conserved in genebanks, such as the Margot Forde Germplasm Centre (MFGC; PalmerstonNorth), are reservoirs of genetic diversity important for the development of cultivars adapted to abiotic stresses and environmental constraints. Genomic tools, including genotyping-by-sequencing (GBS), can support identification of manageable subsets (core collections) that are genetically representative of these large germplasm collections, for phenotypic characterisation. We used GBS to generate SNP (single nucleotide polymorphism) profiles for 172 white clover (WC) and 357 perennial ryegrass (PRG) MFGC-sourced accessions and estimated genetic relationships amongst accessions. In WC, accessions aligned along an east-west transect from Kazakhstan to Spain, identifying major diversity in Caucasus/Central Asia and Iberian Peninsula. A key feature was the reduced diversity present in New Zealand (NZL) accessions. Similarly, for PRG, most NZL accessions coalesced as one group, distinct from large clusters associated with the Iberian Peninsula, Italy and eastern Mediterranean/Caucasian region. These results emphasise the relatively narrow genetic diversity in NZL WC and PRG, and the broad extent of largely unexploited global diversity. Capturing global genetic variation incore collections will support pre-breeding programmes to mobilise novel genetic variation into New Zealand-adapted genetic backgrounds, enabling development of cultivars with non-traditional traits including enhancedclimate resilience and environmental performance.

Pedigree analysis of pre-breeding efforts in Trifolium spp. germplasm in New Zealand

BackgroundPrebreeding in plants is the activity designed to identify useful characteristics from wild germplasm and its integration in breeding programs. Prebreeding aims to introduce new variation into the populations of a species of interest. Pedigree analysis is a valuable tool for evaluation of variation in genebanks where pedigree maps are used to visualize and describe population structure and variation within these populations. Margot Forde Germplasm Centre (MFGC) is New Zealand’s national forage genebank and holds a collection of ~ 75 species of the genus Trifolium, of which only a dozen have been taken through prebreeding programs. The main objective of this study was to construct pedigree maps and analyse patterns of relatedness for seven minor Trifolium species accessions contained at the MFGC. These species are Trifolium ambiguum, Trifolium arvense, Trifolium dubium, Trifolium hybridum, Trifolium medium, Trifolium subterraneum and the Trifolium repens x Trifolium occidentale interspecific hybrids. We present a history of Trifolium spp. prebreeding in New Zealand and inform breeders of possible alternative forage species to use.ResultsPedigree data from accessions introduced between 1950 and 2016 were used and filtered based on breeding activity. Kinship levels among Trifolium spp. remained below 8% and no inbreeding was found. Influential ancestors that contributed largely to populations structure were identified. The Australian cultivar ‘Monaro’ had a strong influence over the whole population of accessions in T. ambiguum. T. subterraneum and T. repens x T. occidentale had the largest number of generations (3). T. ambiguum and T. medium had the highest cumulative kinship across the decades.ConclusionsWe conclude that there are high levels of diversity in the seven Trifolium spp. studied. However, collection and prebreeding efforts must be strengthened to maximize utilization and bring useful genetic variation.

Screening cultivated eggplant and wild relatives for resistance to sweetpotato whitefly (Bemisia tabaci) and to two-spotted spider mite (Tetranychus urticae)

Whiteflies and spider mites are amongst the most harmful eggplant (Solanum melongena) pests. Considering the need for reduction of chemical applications for whitefly and spider mite control, the exploitation of wild relatives of eggplant as sources of pest resistances represents an important strategy in order to improve cultivated eggplant. The objectives of this study were to evaluate 15 accessions from 11 species of eggplant wild relatives together with seven S. melongena accessions for resistance to sweet potato whitefly (Bemisia tabaci) and to two-spotted spider mite (Tetranychus urticae). Resistance to whitefly was evaluated based on number of eggs, nymph, puparium and whitefly adults in a choice bioassay, while for two-spotted spider mite it was based on leaf damage scores in the choice and no-choice bioassays. The results revealed significantly (P < 0.05) different levels of resistance to the two pests among the accessions evaluated. Considering all screening parameters in the whitefly choice bioassay, the highest levels of resistance in wild eggplant relatives were detected in Solanum dasyphyllum (DAS1) and S. pyracanthos (PYR1), although one of the cultivated S. melongena (MEL2) accessions also displayed similar resistance levels. In addition, S. campylacanthum (CAM8) and S. tomentosum TOM1 were also resistant to whitefly based on numbers of puparium and adult whiteflies. Two accessions of S. sisymbriifolium (SIS1 and SIS2) exhibited strong resistance to two-spotted spider mite based on the choice and no-choice bioassays. High levels of spider mite resistance were also detected in the no-choice assay in S. dasyphyllum (DAS1) and S. torvum (TOR2) accessions. These resistant accessions can be used in pre-breeding program aiming to breed pest-resistant cultivars in cultivated eggplant. Moreover, to our knowledge, this study represents the first report on potential sources of resistance to whitefly and two-spotted spider mite in wild relatives of eggplant.

Quo vadis wheat breeding: a case study in Central Europe

Bread wheat (Triticum aestivum) is one of the most important crop species. It has been further developed since its initial domestication, with significant acceleration of wheat breeding within the last 100 years. In this study, a set of 355 wheat accessions were selected to document the history of bread wheat breeding in Central Europe. Although six periods of breeding were assumed, a notable turning point was identified between periods 3 and 4 around the year 1970 based on phenotype and genotype data, dividing the more than 100 years of bread wheat breeding into only two periods. While the first period corresponded to the use of landraces and genetically diverse varieties for breeding, the second period was typically characterized by reliance on relatively few varieties, leading to modern varieties with very good yields and high resistance to lodging and powdery mildew. A drawback of these breeding programmes was a substantial reduction in genetic diversity. The analysis of population structure showed that genetic diversity is influenced more by pedigree than by the period of breeding. In total, five genetic populations were identified, corresponding (especially within the last 50 years) to the leading genotypes used in breeding programmes: Bankuti 1205, Mironovskaja 808 and Moisson. A high level of correlation was found between the genotype and phenotype data (R = 0.91; p < 0.01). The results of this study indicated the need to broaden the genetic diversity of bread wheat by including landraces and possibly wild relatives of crops in new breeding or prebreeding programmes.

Root phenotypes at maturity in diverse wheat and triticale genotypes grown in three field experiments: Relationships to shoot selection, biomass, grain yield, flowering time, and environment

Abstract Modelling and limited data suggest that crops with deeper and longer roots capture more soil resources and yield more when water is available deeper in soil profiles. Interest has grown in the development of new cultivars with deeper roots. This study provides data from three field experiments to help researchers and breeders continue to assess the value of selecting for deeper roots for yield and water use efficiency gains. We asked: do genotype groups with shoot phenotypes easily selectable in pre-breeding programs express predictable root depth and length at time of grain harvest in the field? Do flowering time and shoot biomass predict deep roots measured directly in the field with coring, such that deeper roots are associated with more shoot growth and yield? Does genotype, including triticale versus wheat types, vary in rooting traits? Thirty-four wheats (Triticum aestivum L.) and two triticales (× Triticosecale) were drawn from ten ‘genotype groups’; selections from breeding programs and commercial cultivars that were distinguished on the basis of height, tillering, winter habit, and early vigour. These were grown at two independent sites and soil conditions in year 1 (experiment 1 and 2), with a subset of six wheats and two triticales repeated in year 2 at year 1 site (experiment 3). Above-ground biomass, flowering date, grain yield and root length and depth were measured with a high level of replication (four replicate plots and four soil cores per plot). Root length density was predicted from root counts obtained using the core-break method on 42 mm diameter, two m deep cores. A Bayesian multivariate mixed-effects model was used with fixed effects of the environment and random effects of genotype groups, genotypes and their interactions with the environment. Variation in rooting depth and length caused by environments was much larger than that caused by genotypes. Positive relationships between biomass, yield and root depth and length were observed across experiments and genotype groups (r = 0.62 for biomass and root depth, r = 0.61 for yield and root depth; r = 0.66 for biomass and root length, r = 0.53 for yield and root length), but the largest effects were driven by differences in soil and rainfall conditions between experiments. However, the smaller genetic effects on rooting depth and yield were positively correlated (r = 0.69). We did not find that easily selectable shoot traits like early vigour, tillering, and height reliably predicted in-field deeper rooting. Notably, the two triticales were 74 % more likely to have a deeper rooting and 82 % more likely to have less total root length, than spring wheats. We conclude that deeper and longer roots at maturity are (1) challenging to pre-select using shoot phenotype prior to field evaluation; (2) depend almost entirely on environment for expression in the field with small effects of genotype; and (3) can grow at no apparent 'cost' to shoot growth or yield and as such can remain a target for breeding.

Development of Triticale × Wheat Prebreeding Germplasm With Loci for Slow-Rusting Resistance.

There is a growing interest in breeding and production of hexaploid triticale (× Triticosecale Wittmack ex A. Camus) in European Union and in the world. It is reported that triticale can be an alternative to wheat (Triticum aestivum L.) for livestock feed production and has a potential to become preferred industrial energy crop. Fungal diseases, mainly leaf and stripe rusts, are the limiting factors of triticale growth and yield. Geneticists and breeders are now focusing on accumulation of the major genes for durability of rust resistance. Slow-rusting genes Lr34/Yr18 and Lr46/Yr19 are being exploited in many wheat breeding programs. This type of horizontal resistance is reported to be effective over space and time. Classical breeding techniques supported by marker-assisted selection (MAS) are the main tools in breeding programs. The aim of this study was to assess the possibility of transfer of slow-rusting genes from resistant genotypes of wheat into hexaploid triticale through cross-hybridizations. A total of 5,094 manual pollinations were conducted between two triticale cultivars Fredro and Twingo and 33 accessions of common wheat, which were reported as sources of slow-rusting resistance genes. The investigation of the slow-rusting gene transmission was performed using both molecular markers analyses and genomic in situ hybridization (GISH). In total, 34 F1 hybrid plants were obtained, and 29 of them carried both slow-rusting loci. Therefore, these hybrids may be used for triticale prebreeding program.

Tapping Pennisetum violaceum, a Wild Relative of Pearl Millet (Pennisetum glaucum), for Resistance to Blast (caused by Magnaporthe grisea) and Rust (caused by Puccinia substriata var. indica).

Blast (Magnaporthe grisea) and rust (Puccinia substriata var. indica) are the two important foliar diseases of pearl millet (Pennisetum glaucum (L.) R. Br.) that can be best managed through host plant resistance. For identification of diverse sources of blast and rust resistance, 305 accessions of Pennisetum violaceum, a wild relative of pearl millet, were screened under greenhouse conditions against five pathotype-isolates of M. grisea and a local isolate of P. substriata var. indica collected from ICRISAT farm, Patancheru, India. Based on the mean blast score (1 to 9 scale), 17 accessions (IP 21525, 21531, 21536, 21540, 21594, 21610, 21640, 21706, 21711, 21716, 21719, 21720, 21721, 21724, 21987, 21988, and 22160) were found resistant (score ≤3.0) to all five pathotypes, and 24 accessions were resistant to four pathotypes of M. grisea. As there was variability for rust resistance within some accessions, individual rust-resistant (<5% severity) plants from 17 accessions were selected, grown in pots and advanced to next generation by selfing, and rescreened for three to four generations following pedigree selection to develop rust-resistant genetic stocks. Single plant selections from nine accessions (IP 21629, 21645, 21658, 21660, 21662, 21711, 21974, 21975, and 22038) were found highly resistant to rust (0% rust severity) after four generations of pedigree selection and subsequent screening. Some of the blast-resistant accessions and rust-resistant genetic stocks are being utilized in a prebreeding program at ICRISAT for introgressing resistance genes from the wild into the parental lines of cultivated and potential pearl millet hybrids and varieties.

Suitability of Single-Nucleotide Polymorphism Arrays Versus Genotyping-By-Sequencing for Genebank Genomics in Wheat.

Genebank genomics promises to unlock valuable diversity for plant breeding but first, one key question is which marker system is most suitable to fingerprint entire genebank collections. Using wheat as model species, we tested for the presence of an ascertainment bias and investigated its impact on estimates of genetic diversity and prediction ability obtained using three marker platforms: simple sequence repeat (SSR), genotyping-by-sequencing (GBS), and array-based SNP markers. We used a panel of 378 winter wheat genotypes including 190 elite lines and 188 plant genetic resources (PGR), which were phenotyped in multi-environmental trials for grain yield and plant height. We observed an ascertainment bias for the array-based SNP markers, which led to an underestimation of the molecular diversity within the population of PGR. In contrast, the marker system played only a minor role for the overall picture of the population structure and precision of genome-wide predictions. Interestingly, we found that rare markers contributed substantially to the prediction ability. This combined with the expectation that valuable novel diversity is most likely rare suggests that markers with minor allele frequency deserve careful consideration in the design of a pre-breeding program.

Wild pea (Pisum sativum L. subsp. elatius (Bieb.) Aschers. et Graebn. s.l.) at the periphery of its range: Zagros Mountains.

Characteristics of wild peas and their habitats at the periphery of the range are interesting with respect to their potential importance for pre-breeding programs aimed at selection for different environmental conditions. However, wild pea diversity in peripheral regions is insufficiently represented in the existing germplasm collections. In such regions, wild pea populations are rare, small in size and suffer from climatic change and land exploitation, hence their focused search is strongly desirable. A two-week-long expedition to Iran in May 2017 revealed two small populations of the wild pea (Pisum sativum subsp. elatius) in the Zagros Mts, in Aligudarz and Khorramabad Districts of Lorestan Province, Iran, at elevations of 1841 and 1971 m a.s.l., respectively. Their habitats are briefly described. Two pea accessions derived from them, CE9 and CE10, were characterised for some visible and molecular characters. These peas appeared to belong to the evolutionary lineage B, recognised by us earlier in P. sativum as opposed to the so-called lineage AC. They contain a unique non-conservative substitution in subtype 5 of histone H1 and turned to be most related to some wild pea accessions originating from southern and south-eastern Turkey and Golan Heights. Scarce information available on wild pea occurrence in Iran suggests their existence in the south-western principal slope of Zagros Mts and southern principal slopes of Elborz and Kopet Dagh Mts. It was found that wild peas representing the evolutionary lineage B produce poorly open and poorly coloured flowers (as reported by us earlier) only in the greenhouse conditions but normally pigmented and open flowers in the wild and mesh houses at open air in Israel. Some issues of pea taxonomy are discussed.

Assessment of Morphological Traits and Fruit Metabolites in Eleven Fig Varieties (Ficus Carica L.)

ABSTRACT In the present study, morphological traits, organic acids, sugars, total phenols, total flavonoids, total anthocyanins, total anthocyanidins, antioxidant activity and color parameters such as lightness(L*), Chroma (c*) and hue angle (h°) were investigated in 11 local and introduced fig cultivars cultivated in Moroccan climate. Since only limited information on that topic is available in the literature, this study was performed in order to compare local clones with some of introduced varieties based on their morphological and biochemical attributes. Results showed highly significant differences among genotypes. The cultivar ‘Kadota’ had the most promising morphological traits. Reducing sugars levels were slightly similar among all cultivars. Thus, glucose varied from 5.55 ± 0.27 to 29.94 ± 0.81 g.kg−1 dw, while fructose amounts were in the range of 6.23 ± 0.28–28.15 ± 0.78 g.kg−1 dw. ‘Palmera’ exhibited the highest level of Malic acid (4.99 ± 0.2 g.kg−1). The latter was predominant in all cultivars. Total phenols, flavonoids and total anthocyanins were, generally, abundant in dark-colored cultivars, while total proanthocyanidins were dominant in light-colored ones. The local cultivars ‘Fassi’ and ‘Noukali’ contained the highest amounts of total phenols and total anthocyanins, respectively (524.74 ± 35.9mg GAE 100 g−1 dw and 23.77 ± 6.41 cyanidin-3-rutinoside/100 gdw). Free radical scavenging activity (DPPH and ABTS) was, generally, higher in light-colored figs, while, ferric reducing ability (FRAP) was generally higher in dark skin-colored cultivars. The study confirmed the effectiveness of combining morphological and biochemical analyses in fig assessment and its use pre-breeding programs of the species in Morocco.

Transference of multiple resistance to peanut through the development of cross-compatible complex hybrids of wild Arachis.

Peanut (Arachis hypogaea L.) is a tetraploid species with an A and B genome, while the majority of wild Arachis species are diploid with distinct genomes. In pre-breeding programs, one way to introgress interesting wild genes into peanut is by producing amphidiploids. This study aimed at the hybridization between distinct amphidiploids and their characterization, to combine high crossability with peanut, observed in some amphidiploids, with high pest and disease resistances observed in others. These new hybrids were called complex hybrids. Four amphidiploids previously obtained were crossed at four different combinations, and the derived complex hybrids were crossed with four peanut cultivars. Morphological, reproductive, chromosome complement, molecular markers for hybrid identification, phytopatological, and entomological characterizations were performed on the complex hybrids. All cross combinations resulted in complex hybrids. One complete complement of each diploid progenitor was confirmed in each hybrid. Plants of six distinct hybrid combinations were obtained between the complex hybrids and peanut. Based on morphological characterization, differences among progenies from distinct cross combinations were observed. Complex hybrids were considered more resistant to all diseases and pests than peanut cultivars. The simultaneous introgression of genes from four wild Arachis species into peanut was possible through the development of complex hybrids.

Spatial and temporal patterns of lodging in grain sorghum (Sorghum bicolor) in Australia

Grown in water-limited environments, sorghum (Sorghum bicolor (L.) Moench) is often exposed to water deficits of varying extent and timing. One of the impacts of water stress on sorghum production is lodging; however, there has been no published study quantifying the temporal and spatial frequency and severity of lodging in grain sorghum in Australia. In this study, we investigated the frequency and severity of lodging, using a dataset of 83 advanced yield-testing trials of the sorghum pre-breeding program grown in the seven major sorghum-production environments in Australia over 14 summer growing seasons. Lodging occurred in most production regions but with varying frequency and severity. Lodging was significantly greater in regions that were more prone to water stress (e.g. Central Highlands in Queensland) and significantly lower in regions that were less likely to suffer from water stress (e.g. Liverpool Plains in northern New South Wale) compared with the overall average across regions. The severity of lodging also varied across regions, with the most severe lodging (&amp;gt;20%) occurring in Central Highlands and Western Downs in Queensland. In addition, seasonal patterns of lodging frequency and severity were also observed. Over the 14 growing seasons, the frequency of lodging varied from 0% to 100%, with the most severe lodging (&amp;gt;20%) observed in 2005, 2016 and 2017. The Southern Oscillation Index explained 29% of the seasonal variation in lodging frequency. The findings of this study clearly support a link between lodging incidence and water stress across regions and seasons. Our data also showed that although there was a substantial turnover of commercial hybrids during the period of this study, the level of resistance to lodging appeared not to have improved. It is possible that this is due to plant breeders trading off improvements in lodging resistance to increase grain yield.

Genetic Diversity of Bertholletia excelsa Bonpl.: A Native Species of the Amazon Rainforest

Abstract In view of the economic and environmental importance of Bertholletia excelsa Bonpl. for the Amazon and the reducing natural habitat area of this species, the present study proposes to examine genetic variability among accessions of Brazil nut from the Amazon rainforest. Seventeen native Brazil nut genotypes were sampled from Sinop-MT and the genomic DNA were amplified using 15 inter-simple sequence repeat (ISSR) markers. The percent polymorphism and the polymorphism information content (PIC) of each primer were determined. The primers amplified 84.62% of the polymorphic bands and 15.38% of the monomorphic bands. The PIC for each primer ranged from 0 to 0.68. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) was the most efficient in group representation, as it showed the highest cophenetic correlation coefficient (CCC = 0.92), the lowest stress (12.31%) and the lowest distortion (1.51%). The use of ISSR markers was an efficient tool in the study of genetic diversity among Brazil nut genotypes, and the genetic diversity found can be used for conservation and pre-breeding programs for this crop.

English

To broaden the genetic base of the allotetraploid peanut (Arachis hypogaea L.), pre-breeding programs have produced interspecific synthetic allotetraploids resulting from the chromosome duplication of hybrids between peanut related diploid species. These allotetraploids were highly cross-fertile with peanut making it possible to access the extensive genetic variability harbored by the wild species. This study aims to evaluate the impact of polyploidization and hybridization in resveratrol content in Arachis hybrids. Resveratrol is a potent antioxidant that has been shown to be useful in the treatment of many human diseases. For that, resveratrol was characterized in five synthetic allotetraploids of wild Arachis, six diploid wild species, three cultivars of A. hypogaea and three backcross (BC) hybrids between synthetic allotetraploids and A. hypogaea. Leaves from these genotypes were ultraviolet (UV) light irradiated for 2 h 30 min and their resveratrol contents were determined by high performance liquid chromatograph (HPLC). Resveratrol was found in all genotypes, but at variable concentrations. Synthetic allotetraploids and peanut did not differ and diploid species had the lowest resveratrol content. The highest concentrations were observed in hybrids between allotetraploids and cultivars of A. hypogaea that were probably the most heterozygous among the genotypes analyzed since their chromosome sets came from different species. This study data suggest a positive effect of polyploidy and hybridization in resveratrol content. Key words: Peanut, wild relatives, polyploidy, pre-breeding.

Harnessing leaf photosynthetic traits and antioxidant defence for multiple stress tolerance in three premium indigenous rice landraces of Jeypore tract of Odisha, India.

The aim of the present research was to compare the effects of different abiotic stresses (drought, salinity and submergence) on growth, photosynthesis and PSII activity along with antioxidant defence of three premium rice landraces, namely Kalajeera, Machhakanta and Haladichudi from Jeypore tract of Odisha, India to evaluate their performance under multiple stresses and possibility of using in the pre-breeding programs. Results showed that drought, salinity and submergence significantly reduced plant growth, leaf photosynthesis, water use efficiency (WUE), carboxylation efficiency (CE), PSII activity and SPAD chlorophyll index, and the highest effect was observed in susceptible check variety (IR64). In addition, the indigenous rice lines showed better stomatal traits such as stomatal density (SD), stomatal size (SS) and stomatal number per leaf area (S/LA). Notably, higher activities of antioxidative enzymes and proline accumulation was observed in studied indigenous rice landraces and were found comparable with the drought and salinity tolerant (N22) and submergence tolerant (FR13A) check varieties. Based on our findings it was revealed that these landraces can be expected to possess an adequate level of tolerance to drought, salinity and submergence and showed adaptive fitness to multiple stresses during seedling stage. These landraces can be considered as potential donor for future rice pre-breeding program.

Root transcriptome analysis of Saccharum spontaneum uncovers key genes and pathways in response to low-temperature stress

Low-temperature (LT) stress is known to restrain sugarcane productivity in sub-tropical regions significantly. Many researchers have prioritized their work towards developing climate-resilient sugarcane varieties incorporating genome of stress-tolerant sugarcane related wild-type species in the pre-breeding programs. However, the lack of genomic resources for wild-type sugarcane limits the identification and utilization of stress-related genes in molecular breeding. In this study, for the first time, we generated ∼182 million RNA-seq paired-end reads for Saccharum spontaneum roots grown under low temperature (10 °C) at different time intervals (0 h, 3 h, 6 h, 12 h, 24 h, and 48 h), to identify LT stress responsive genes and pathways. These data were assembled into 141,409 unigenes and subsequently used to identify 2715 upregulated and 1710 downregulated transcripts under LT stress. Combining evidences from GO enrichment, KEGG pathways, histological studies, biochemical assays, and physiological analysis, our results revealed several key genes and pathways involved in cold acclimatization in the S. spontaneum roots. Transcription profiling of roots during LT stress revealed cold stress sensors (i.e., proline, MDA, calcium-dependent kinase, G-coupled proteins, and histidine kinase) that trigger and activate signal transduction through transcription factors (i.e., MYB, ERF, ARF2, DREB, CAMTA, and C2H2) resulting in upregulation of LT stress responsive genes (i.e, annexin, LEA, germins, LT dehydrins, osmotins, and COR) thereby enhancing cold tolerance. Also, transcriptomic analysis envisaged cold responsive metabolic pathways such as phenylpropanoid and sugar metabolism stimulate the synthesis of flavonoid, sucrose, galactose, raffinose, and fructose, antioxidants, phytohormones, and secondary metabolites, and thus trigger cold-responsive transcriptional regulation. Together, this study provides insights into cold tolerance of wild sugarcane roots to LT stress, thus providing a foundation for developing climate-resilient sugarcane varieties.