Theoretical and experimental assessment of genome-based prediction in landraces of allogamous crops.

Discovery and enrichment of favorable alleles in landraces are key to making them accessible for crop improvement. Here, we present two fundamentally different concepts for genome-based selection in landrace-derived maize populations, one based on doubled-haploid (DH) lines derived directly from individual landrace plants and the other based on crossing landrace plants to a capture line. For both types of populations, we show theoretically how allele frequencies of the ancestral landrace and the capture line translate into expectations for molecular and genetic variances. We show that the DH approach has clear advantages over gamete capture with generally higher prediction accuracies and no risk of masking valuable variation of the landrace. Prediction accuracies as high as 0.58 for dry matter yield in the DH population indicate high potential of genome-based selection. Based on a comparison among traits, we show that the genetic makeup of the capture line has great influence on the success of genome-based selection and that confounding effects between the alleles of the landrace and the capture line are best controlled for traits for which the capture line does not outperform the ancestral population per se or in testcrosses. Our results will guide the optimization of genome-enabled prebreeding schemes.

Characterization of indigenous populations of cannabis in Iran: a morphological and phenological study.

BACKGROUND: Cannabis is a historically, culturally, and economically significant crop in human societies, owing to its versatile applications in both industry and medicine. Over many years, native cannabis populations have acclimated to the various environments found throughout Iran, resulting in rich genetic and phenotypic diversity. Examining phenotypic diversity within and between indigenous populations is crucial for effective plant breeding programs. This study aimed to classify indigenous cannabis populations in Iran to meet the needs of breeders and breeding programs in developing new cultivars. RESULTS: Here, we assessed phenotypic diversity in 25 indigenous populations based on 12 phenological and 14 morphological traits in male and female plants. The extent of heritability for each parameter was estimated in both genders, and relationships between quantitative and time-based traits were explored. Principal component analysis (PCA) identified traits influencing population distinctions. Overall, populations were broadly classified into early, medium, and late flowering groups. The highest extent of heritability of phenological traits was found in Start Flower Formation Time in Individuals (SFFI) for females (0.91) Flowering Time 50% in Individuals (50% of bracts formed) (FT50I) for males (0.98). Populations IR7385 and IR2845 exhibited the highest commercial index (60%). Among male plants, the highest extent of Relative Growth Rate (RGR) was observed in the IR2845 population (0.122 g.g- 1.day- 1). Finally, populations were clustered into seven groups according to the morphological traits in female and male plants. CONCLUSIONS: Overall, significant phenotypic diversity was observed among indigenous populations, emphasizing the potential for various applications. Early-flowering populations, with their high RGR and Harvest Index (HI), were found as promising options for inclusion in breeding programs. The findings provide valuable insights into harnessing the genetic diversity of indigenous cannabis for diverse purposes.

Physiological and Molecular Mechanisms Associated with Potato Tuber Dormancy.

Tuber dormancy is an important physiological trait that impacts postharvest storage and end use qualities of potatoes. Overall, dormancy regulation of potato tuber is a complex process driven by genetic as well as environmental factors. Elucidation of the molecular and physiological mechanisms that influence different dormancy stages of tuber has wider potato breeding and industry relevant implications. Therefore, the primary objective of this review is to present the current knowledge on the diversity in tuber dormancy traits among wild relatives of potatoes and discuss how genetic and epigenetic factors contribute to the tuber dormancy. Advancements in understanding of key physiological mechanisms involved in tuber dormancy regulations, such as apical dominance, phytohormone metabolism, and oxidative stress responses were also discussed. This review highlights the impacts of common sprout suppressors on the molecular and physiological mechanisms associated with tuber dormancy and other storage qualities. Collectively, the literature suggests that significant changes in expressions of genes associated with cell cycle, phytohormone metabolism, and oxidative stress response influence initiation, maintenance, and termination of dormancy in potato tubers. Commercial sprout suppressors mainly alter the expressions of genes associated with cell cycle and stress responses and suppress sprout growth rather than prolonging the tuber dormancy.

Assessing genetic, racial, and geographic diversity among Ethiopian sorghum landraces and implications for heterotic potential for hybrid sorghum breeding.

The wealth of sorghum genetic resources in Africa has not been fully exploited for cultivar development in the continent. Hybrid cultivars developed from locally evolved germplasm are more likely to possess a well-integrated assembly of genes for local adaptation, productivity, quality, as well as for defensive traits and broader stability. A subset of 560 sorghum accessions of known fertility reaction representing the major botanical races and agro-ecologies of Ethiopia were characterized for genetic, agronomic and utilization parameters to lay a foundation for cultivar improvement and parental selection for hybrid breeding. Accessions were genotyped using a genotyping by sequencing (GBS) generating 73,643 SNPs for genetic analysis. Significant genetic variability was observed among accessions with Admixture and Discriminant Analysis of Principal Components where 67% of the accessions fell into K=10 clusters with membership coefficient set to > 0.6. The pattern of aggregation of the accessions partially overlapped with racial category and agro-ecological adaptation. Majority of the non-restorer (B-line) accessions primarily of the bicolor race from the wet highland ecology clustered together away from two clusters of fertility restorer (R-line) accessions. Small members of the B accessions were grouped with the R clusters and in vice-versa while significant numbers of both B and R accessions were spread between the major clusters. Such pattern of diversity along with the complementary agronomic data based information indicate the potential for heterosis providing the foundation for initiating hybrid breeding program based on locally adapted germplasm. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01483-8.

Unlocking the story of resistance to Zymoseptoria tritici in Tunisian old durum wheat germplasm based on population structure analysis.

BACKGROUND: Septoria tritici blotch (STB) remains a significant obstacle to durum wheat cultivation on a global scale. This disease remains a challenge for farmers, researchers, and breeders, who are collectively dedicated to reduce its damage and improve wheat resistance. Tunisian durum wheat landraces have been recognized as valuable genetic ressources that exhibit resistance to biotic and abiotic stresses and therefore play a crucial role in breeding program aimed at creating new wheat varieties resistant to fungal diseases as STB, as well as adapted to climate change constraints. RESULTS: A total of 366 local durum wheat accessions were assessed for resistance to two virulent Tunisian isolates of Zymoseptoria tritici Tun06 and TM220 under field conditions. Population structure analysis of the durum wheat accessions, performed with 286 polymorphic SNPs (PIC > 0.3) covering the entire genome, identified three genetic subpopulations (GS1, GS2 and GS3) with 22% of admixed genotypes. Interestingly, all of the resistant genotypes were among GS2 or admixed with GS2. CONCLUSIONS: This study revealed the population structure and the genetic distribution of the resistance to Z. tritici in the Tunisian durum wheat landraces. Accessions grouping pattern reflected the geographical origins of the landraces. We suggested that GS2 accessions were mostly derived from eastern Mediterranean populations, unlike GS1 and GS3 that originated from the west. Resistant GS2 accessions belonged to landraces Taganrog, Sbei glabre, Richi, Mekki, Badri, Jneh Khotifa and Azizi. Furthermore, we suggested that admixture contributed to transmit STB resistance from GS2 resistant landraces to initially susceptible landraces such as Mahmoudi (GS1), but also resulted in the loss of resistance in the case of GS2 susceptible Azizi and Jneh Khotifa accessions.

Phenotypic characterization and seed viability test in ex-situ conserved Ethiopian cultivated barley (Hordeum vulgare L.) landraces.

BACKGROUND: Nowadays, most of the Ethiopian barley landraces had been lost from farmer's field and exclusively found ex-situ conserved at the Ethiopian Biodiversity Institute (EBI). Those ex-situ conserved are generally believed to be representative of the original population and possess high genetic diversity and important unique genes that are useful for tackling the various biotic and abiotic stresses in the face of the current climate change. Thus, this research was aimed at testing the performance of 150 ex-situ conserved landraces that had been collected from Arsi and Bale highlands, Southeastern Ethiopia. The landraces were tested at multiple test locations over two years (2021 and 2022). RESULTS: All the tested landraces showed a good germination rate regardless of their long storage duration. In addition, performance of all the qualitative traits revealed a varying frequency for each character state. For example, most of the accessions (51.3%) had six kernel row numbers (KRN). All the remaining accessions had two rows (28.7%) and irregular KRN with variable lateral florets (20%). Likewise, some of the quantitative traits considered showed a significant variation among the landraces. However, there observed a significant variation for all the interaction effects in some of the traits considered signifying the importance of considering environment effects while targeting genetic selection and improvement of ex-situ conserved germplasms. The phenotypic coefficients of variation (PCV) were considerably high to medium in most of the traits considered including seed yield per hectare (SYPH) but with no associated higher genotypic coefficients of variation (GCV). Moreover, all the traits showed a far greater phenotypic coefficient of variation (PCV) to that of genotypic coefficients of variation (GCV) once again suggesting the pronounced effect of environmental factors to the variation. This was far supported by the significantly higher absolute magnitudes in phenotypic correlation compared to their corresponding genotypic correlation in most of the traits. Low estimates of heritability and genetic advance observed in all the traits considered except seed yield per hectare indicate importance of the trait for selection in Ethiopian barley improvement programs. Clustering patterns of the accessions, in narrow sense, revealed the existence of low divergence among the samples. CONCLUSION: Ethiopian barley landraces are promising candidates for further yield improvement and conservation. However, further regular testing and screening should be conducted for the ex-situ conserved landraces because of the current erratic climate change. In addition, more robust molecular marker systems could be used to clearly reveal the extents of genetic diversity and to facilitate the breeding and conservation of Ethiopian barley landraces.

A high-quality assembled genome of a representative peach landrace, 'Feichenghongli', and analysis of distinct late florescence and narrow leaf traits.

BACKGROUND: Peach (Prunus persica L. Batsch) is one of the most popular fruits worldwide. Although the reference genome of 'Lovell' peach has been released, the diversity of genome-level variations cannot be explored with one genome. To detect these variations, it is necessary to assemble more genomes. RESULTS: We sequenced and de novo assembled the genome of 'Feichenghongli' (FCHL), a representative landrace with strict self-pollination, which maintained the homozygosity of the genome as much as possible. The chromosome-level genome of FCHL was 239.06 Mb in size with a contig N50 of 26.93 Mb and only 4 gaps at the scaffold level. The alignment of the FCHL genome with the reference 'Lovell' genome enabled the identification of 432535 SNPs, 101244 insertions and deletions, and 7299 structural variants. Gene family analysis showed that the expanded genes in FCHL were enriched in sesquiterpenoids and triterpenoid biosynthesis. RNA-seq analyses were carried out to investigate the two distinct traits of late florescence and narrow leaves. Two key genes, PpDAM4 and PpAGL31, were identified candidates for the control of flower bud dormancy, and an F-box gene, PpFBX92, was identified as a good candidate gene in the regulation of leaf size. CONCLUSIONS: The assembled high-quality genome could deepen our understanding of variations among diverse genomes and provide valuable information for identifying functional genes and improving the molecular breeding process.

Water stress effects on stay green and chlorophyll fluorescence with focus on yield characteristics of diverse bread wheats.

MAIN CONCLUSION: The study provided an insight toward better understanding of stay-green mechanisms for drought tolerance improvement and identified that synthetic-derived wheats proved as a promising germplasm for improved tolerance against water stress. Stay-green (SG) trait is considered to be related with the ability of wheat plants to maintain photosynthesis and CO2 assimilation. The present study explored the interaction of water stress with SG expression through physio-biochemical, agronomic and phenotypic responses among diverse wheat germplasm comprising of 200 synthetic hexaploids, 12 synthetic derivatives, 97 landraces and 16 conventional bread wheat varieties, for 2 years. The study established that variation of SG trait existed in the studied wheat germplasm and there was positive association between SG trait and tolerance to water stress. The relationship of SG trait with chlorophyll content (r = 0.97), ETR (r = 0.28), GNS (r = 0.44), BMP (r = 0.34) and GYP (r = 0.44) was particularly promising under water stress environment. Regarding chlorophyll fluorescence, the positive correlation of фPSII (r = 0.21), qP (r = 0.27) and ETR (r = 0.44) with grain yield per plant was noted. The improved ΦPSII and Fv/Fm of PSII photochemistry resulted in the high photosynthesis activity in SG wheat genotypes. Regarding relative water content and photochemical quenching coefficient, synthetic-derived wheats were better by maintaining 20.9, 9.8 and 16.1% more RWC and exhibiting 30.2, 13.5 and 17.9% more qP when compared with landraces, varieties and synthetic hexaploids, respectively, under water stress environment. Synthetic derived wheats also exhibited relatively more SG character with good yield and were more tolerant to water stress in terms of grain yield, grain weight per plant, better photosynthetic performance through chlorophyll fluorescence measurement, high leaf chlorophyll and proline content, and hence, may be used as novel sources for breeding drought tolerant materials. The study will further facilitate research on wheat leaf senescence and will add to better understanding of SG mechanisms for drought tolerance improvement.

Evolution of the rice blast pathogen on spatially structured rice landraces maintains multiple generalist fungal lineages.

Traditional agrosystems, where humans, crops and microbes have coevolved over long periods, can serve as models to understand the ecoevolutionary determinants of disease dynamics and help the engineering of durably resistant agrosystems. Here, we investigated the genetic and phenotypic relationship between rice (Oryza sativa) landraces and their rice blast pathogen (Pyricularia oryzae) in the traditional Yuanyang terraces of flooded rice paddies in China, where rice landraces have been grown and bred over centuries without significant disease outbreaks. Analyses of genetic subdivision revealed that indica rice plants clustered according to landrace names. Three new diverse lineages of rice blast specific to the Yuanyang terraces coexisted with lineages previously detected at the worldwide scale. Population subdivision in the pathogen population did not mirror pattern of population subdivision in the host. Measuring the pathogenicity of rice blast isolates on landraces revealed generalist life history traits. Our results suggest that the implementation of disease control strategies based on the emergence or maintenance of a generalist lifestyle in pathogens may sustainably reduce the burden of disease in crops.

Plant host domestication and soil nutrient availability determine positive plant microbial response across the Solanum genus.

Domestication of crops has changed how crops shape their associated microbial communities compared with their progenitors. However, studies testing how crop domestication-driven differences in rhizosphere microbial communities affect plant health are limited mostly to specific symbiont pairings. By conducting a soil manipulation greenhouse study, we examined plant growth and yield in response to differences in microbial communities and nutrient availability across a variety of wild, landrace, and commercially available 'Modern' potatoes. Coupled with this, we conducted 16S and internal transcribed spacer (ITS) amplicon sequencing to examine plant host- and soil treatment-driven differences in microbial community composition on potato plant roots. We found that the plant response to microbes (PRM) was context dependent. In low nutrient conditions, landraces responded positively to the presence of live soil microbial inocula. Conversely, modern potato varieties responded positively only in high nutrient conditions. Amplicon sequencing found differences in bacterial communities due to environmental and temporal factors. However, potato clade (e.g. Andigenum, Chiletanum, Solanum berthaultii, and 'Modern') alone did not lead to differences in microbial communities that accounted for PRM differences. Differences in PRM between landraces and modern potatoes, and the correlation of PRM to microbial diversity, suggest that domestication and subsequent breeding have altered the S. tuberosum response to rhizosphere microbiomes between Andigenum, Chiletanum, and North American potato varieties.

The genomic and bioclimatic characterization of Ethiopian barley (Hordeum vulgare L.) unveils challenges and opportunities to adapt to a changing climate.

The climate crisis is impacting agroecosystems and threatening food security of millions of smallholder farmers. Understanding the potential for current and future climatic adaptation of local crop agrobiodiversity may guide breeding efforts and support resilience of agriculture. Here, we combine a genomic and climatic characterization of a large collection of traditional barley varieties from Ethiopia, a staple for local smallholder farmers cropping in challenging environments. We find that the genomic diversity of barley landraces can be partially traced back to geographic and environmental diversity of the landscape. We employ a machine learning approach to model Ethiopian barley adaptation to current climate and to identify areas where its existing diversity may not be well adapted in future climate scenarios. We use this information to identify optimal trajectories of assisted migration compensating to detrimental effects of climate change, finding that Ethiopian barley diversity bears opportunities for adaptation to the climate crisis. We then characterize phenology traits in the collection in two common garden experiments in Ethiopia, using genome-wide association approaches to identify genomic loci associated with timing of flowering and maturity of the spike. We combine this information with genotype-environment associations finding that loci involved in flowering time may also explain environmental adaptation. Our data show that integrated genomic, climatic, and phenotypic characterizations of agrobiodiversity may provide breeding with actionable information to improve local adaptation in smallholder farming systems.

Large scale sampling of Mexican maize landraces for the presence of transgenes.

The presence and levels of transgenic maize in Mexico and the effect this could have on local landraces or closely related species such as teosinte has been the subject of several previous reports, some showing contrasting results. Cultural, social and political factors all affect maize cultivation in Mexico and although since 1998 there has been a moratorium on the commercial cultivation of transgenic maize, Mexico imports maize, mainly from the USA where transgenic cultivars are widely grown. Additionally extensive migration between rural areas in Mexico and the USA and customs of seed exchange between farmers may also play an unintentional role in the establishment of transgenic seed. A comprehensive study of all Mexican maize landraces throughout the country is not feasible, however this report presents data based on analysis of 3204 maize accessions obtained from the central region of Mexico (where permits have never been authorized for cultivation of transgenic maize) and the northern region (where for a short period authorization for experimental plots was granted). The results of the study confirm that transgenes are present in all the geographical areas sampled and were more common in germplasm obtained in the northern region. However, there was no evidence that regions where field trials had been authorized showed higher levels of transgene presence or that the morphology of seed lots harboring transgenic material was significantly modified in favor of expected transgenic phenotypes.

Morpho-physiological traits and SSR markers-based analysis of relationships and genetic diversity among fodder maize landraces in India.

BACKGROUND: Maize is an excellent fodder crop due to its high biomass, better palatability, succulency, and nutrition. Studies on morpho-physiological and biochemical characterization of fodder maize are limited. The present study aimed to explore the genetic variation in fodder maize landraces for various morpho-physiological traits and estimation of genetic relationship and population structure. METHODS AND RESULTS: The study on 47 fodder maize landraces revealed significant variation for all morpho-physiological traits except leaf-stem ratio. Plant height, stem girth, leaf-width and number of leaves showed positive correlation with green fodder yield. Morpho-physiological traits-based clustering grouped the landraces into three major clusters, whereas neighbour joining cluster and population structure analysis using 40 SSR markers revealed four and five major groups, respectively. Most landraces of Northern Himalaya-Kashmir and Ludhiana fall into a single group, whereas rest groups mainly had landraces from North-Eastern Himalaya. A total of 101 alleles were generated with mean polymorphic information content value of 0.36 and major allele frequency of 0.68. The pair wise genetic dissimilarity between genotypes ranged from 0.21 to 0.67. Mantel test revealed weak but significant correlation between morphological and molecular distance. Biochemical characterisation of superior landraces revealed significant variation for neutral detergent fibre, acid detergent fibre, cellulose and lignin content. CONCLUSION: Interestingly, significant, and positive correlation of SPAD with lignin content can be explored to bypass the costly affair of invitro quality assessment for digestibility parameters. The study identified superior landraces and demonstrated the use of molecular markers in genetic diversity assessment and grouping of genotypes for fodder maize improvement.

Genetic potential of grain-related traits in rice landraces: phenomics and multi-locus association analyses.

BACKGROUND: Grain length, width, weight, and the number of grains per panicle are crucial determinants contributing to yield in cereal crops. Understanding the genetic basis of grain-related traits has been the main research object in crop science. METHODS AND RESULTS: Kerala has a collection of different rice landraces. Characterization of these valuable genetic resources for 39 distinct agro-morphological traits was carried out in two seasons from 2017 to 2019 directly in farmers field. Most characteristics were polymorphic except ligule shape, leaf angle, and panicle axis. The results of principal component analysis implied that leaf length, plant height, culm length, flag leaf length, and grain-related traits were the principal discriminatory characteristics of rice landraces. For identifying the genetic basis of key grain traits of rice, three multi locus GWAS models were performed based on 1,47,994 SNPs in 73 rice accessions. As a result, 48 quantitative trait nucleotides (QTNs) were identified to be associated with these traits. After characterization of their function and expression, 15 significant candidate genes involved in regulating grain width, number of grains per panicle, and yield were identified. CONCLUSIONS: The detected QTNs and candidate genes in this study could be further used for marker-assisted high-quality breeding of rice.

Morpho-physiological profiling of rice (Oryza sativa) genotypes at germination stage with contrasting tolerance to salinity stress.

Salinity is among the harshest environmental stress conditions that negatively affects productivity of salt-sensitive rice. Since, germination is the most crucial phase in the life-cycle of plants, the present study was carried out to study the morpho-physiological traits associated with salinity stress. Evaluation of tolerance in four contrasting rice genotypes was assessed on the basis of specific morpho-physiological parameters including radicle emergence, seedling vigour index, germination index, mean germination time, radicle and plumule growth and seedling water uptake. Largely, our findings revealed that mean germination time (MGT) and seedling vigour index (SVI) are fast-screening procedures to test seedling performance in salt stress conditions. Salt sensitive genotypes showed higher MGT and lower SVI, confirming that these indices are good indicators of poor germination response. Salt-tolerant genotypes were shown to be inhibited to a lesser extent in alpha-amylase activity in spite of high concentrations of imposed NaCl stress, that correlated with better regulation of water-uptake and increased accumulation of total soluble sugar content. Exogenous supplementation of soluble sugars improved the germination rate in a salt sensitive genotype, Jyothi, confirming the importance of soluble sugars in signaling under NaCl stress conditions. Increased total phenols and flavonoids were observed to be relative to higher Total Antioxidant Capacity in salt tolerant genotypes underlying the significance of seed phenolic compounds in early germination response in NaCl stress conditions. Kagga, a landrace grown in coastal Karnataka performed comparably with that of salt tolerant rice, Pokkali. In conclusion, the determination of early seedling response may be utilized as a useful strategy to uncover genetic variation in rice germplasm to salinity stress.

Discovering Loci for Breeding Prospective and Phenology in Wheat Mediterranean Landraces by Environmental and eigenGWAS.

Knowledge of the genetic basis of traits controlling phenology, differentiation patterns, and environmental adaptation is essential to develop new cultivars under climate change conditions. Landrace collections are an appropriate platform to study the hidden variation caused by crop breeding. The use of genome-wide association analysis for phenology, climatic data and differentiation among Mediterranean landraces led to the identification of 651 marker-trait associations that could be grouped in 46 QTL hotspots. A candidate gene analysis using the annotation of the genome sequence of the wheat cultivar 'Chinese Spring' detected 1097 gene models within 33 selected QTL hotspots. From all the gene models, 42 were shown to be differentially expressed (upregulated) under abiotic stress conditions, and 9 were selected based on their levels of expression. Different gene families previously reported for their involvement in different stress responses were found (protein kinases, ras-like GTP binding proteins and ethylene-responsive transcription factors). Finally, the synteny analysis in the QTL hotspots regions among the genomes of wheat and other cereal species identified 23, 21 and 7 ortho-QTLs for Brachypodium, rice and maize, respectively, confirming the importance of these loci.

In search of better snacks: ohmic-heating nixtamalized flour and amaranth addition increase the nutraceutical and nutritional potential of vegetable-enriched tortilla chips.

BACKGROUND: Nixtamalized flour snacks such as tortilla chips are widely consumed across the world, but they are nutritionally poor and contribute to obesity and other non-communicable diseases. The production of healthy versions of such snacks, by incorporating vegetables and improving the quality of the flours used in their formulation, could help address these nutritional challenges. This study compared the fortification of baked tortilla chips with vegetable leaf powders (kale and wild amaranth at 0%, 4%, 8%, and 16% w/w) and using two types of nixtamalized flour: traditional (TNF) and with ohmic heating (OHF). RESULTS: Overall, the use of OHF increased 1.88 times the fibre in enriched and non-enriched snacks with respect to TNF, but the latter had 1.85 times more protein. Addition of 16% of vegetable powders increased protein (kale = 1.4-fold; amaranth = 1.3-fold) and dietary fibre (kale = 1.52-fold; amaranth = 1.7-fold). Amaranth enrichment improved total phenolic content (TPC) and total flavonoid content (TFC) of chips at least 1.2 and 1.63 times, respectively. OHF chips also had higher bound TPC than TNF ones, regardless of vegetable addition. Combinations of OHF with 16% amaranth produced chips 1.74-fold higher in antioxidant capacity than non-enriched ones, due to increased content of phenolics such as ferulic acid. CONCLUSION: This work showed that tortilla chips made using nixtamalized flour produced with assisted ohmic heating, alone or in combination with wild amaranth leaf powder, could be used in the production of healthy maize snacks to enhance their prospective antioxidant activity and nutritional value. © 2023 Society of Chemical Industry.

Deciphering resistance to Zymoseptoria tritici in the Tunisian durum wheat landrace accession 'Agili39'.

BACKGROUND: Septoria tritici blotch (STB), caused by Zymoseptoria tritici (Z. tritici), is an important biotic threat to durum wheat in the entire Mediterranean Basin. Although most durum wheat cultivars are susceptible to Z. tritici, research in STB resistance in durum wheat has been limited. RESULTS: In our study, we have identified resistance to a wide array of Z. tritici isolates in the Tunisian durum wheat landrace accession 'Agili39'. Subsequently, a recombinant inbred population was developed and tested under greenhouse conditions at the seedling stage with eight Z. tritici isolates and for five years under field conditions with three Z. tritici isolates. Mapping of quantitative trait loci (QTL) resulted in the identification of two major QTL on chromosome 2B designated as Qstb2B_1 and Qstb2B_2. The Qstb2B_1 QTL was mapped at the seedling and the adult plant stage (highest LOD 33.9, explained variance 61.6%), conferring an effective resistance against five Z. tritici isolates. The Qstb2B_2 conferred adult plant resistance (highest LOD 32.9, explained variance 42%) and has been effective at the field trials against two Z. tritici isolates. The physical positions of the flanking markers linked to Qstb2B_1 and Qstb2B_2 indicate that these two QTL are 5 Mb apart. In addition, we identified two minor QTL on chromosomes 1A (Qstb1A) and chromosome 7A (Qstb7A) (highest LODs 4.6 and 4.0, and explained variances of 16% and 9%, respectively) that were specific to three and one Z. tritici isolates, respectively. All identified QTL were derived from the landrace accession Agili39 that represents a valuable source for STB resistance in durum wheat. CONCLUSION: This study demonstrates that Z. tritici resistance in the 'Agili39' landrace accession is controlled by two minor and two major QTL acting in an additive mode. We also provide evidence that the broad efficacy of the resistance to STB in 'Agili 39' is due to a natural pyramiding of these QTL. A sustainable use of this Z. tritici resistance source and a positive selection of the linked markers to the identified QTL will greatly support effective breeding for Z. tritici resistance in durum wheat.

Genetic diversity and population structure of rice (Oryza sativa L.) landraces from Kerala, India analyzed through genotyping-by-sequencing.

Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for developing dominant strategies for the sustainable management of genetically diverse crops. We attempt to fill the existing research lacuna in the molecular characterization of potent rice landraces in Kerala. Genotyping-by-sequencing (GBS) was performed on 96 Kerala rice accessions to identify single-nucleotide polymorphisms (SNPs), to examine the genetic diversity, population structure, and to delineate linkage disequilibrium (LD) pattern. GBS identified 5856 high-quality SNPs. The structure analysis indicated three subpopulations with the highest probability for population clustering with significant genetic differentiation, confirmed by principal component analysis. The genome-wide LD decay distance was 772 kb, at which the r2 dropped to half its maximum value. The analysis of genetic properties of the identified SNP panel with an average polymorphism information content (PIC) value of 0.22 and a minor allele frequency (MAF) > 0.1 unveiled their efficacy in genome-wide association studies (GWAS). High FST (0.266) and low Nm (0.692) portray a strong genetic differentiation among the rice landraces, complementing the genetic structuring observed in the studied population. Slow LD decay in the rice landraces reflects their self-pollinating behavior and the indirect selection of desired traits by domestication. Moreover, the high LD entails only a minimum number of SNP markers for detecting marker-trait association. The diverse germplasm utilized in this study can be further utilized to disclose genetic variants associated with phenotypic traits and define signatures of selection via GWAS and selective sweep, respectively.

Crop genetic erosion: understanding and responding to loss of crop diversity.

Crop diversity underpins the productivity, resilience and adaptive capacity of agriculture. Loss of this diversity, termed crop genetic erosion, is therefore concerning. While alarms regarding evident declines in crop diversity have been raised for over a century, the magnitude, trajectory, drivers and significance of these losses remain insufficiently understood. We outline the various definitions, measurements, scales and sources of information on crop genetic erosion. We then provide a synthesis of evidence regarding changes in the diversity of traditional crop landraces on farms, modern crop cultivars in agriculture, crop wild relatives in their natural habitats and crop genetic resources held in conservation repositories. This evidence indicates that marked losses, but also maintenance and increases in diversity, have occurred in all these contexts, the extent depending on species, taxonomic and geographic scale, and region, as well as analytical approach. We discuss steps needed to further advance knowledge around the agricultural and societal significance, as well as conservation implications, of crop genetic erosion. Finally, we propose actions to mitigate, stem and reverse further losses of crop diversity.