Application of near-infrared spectroscopy for fast germplasm analysis and classification in multi-environment using intact-seed peanut(Arachis hypogaea L.)

Peanut is a worldwide oilseed crop and the need to assess germplasm in a non-destructive manner is important for seed nutritional breeding.In this study,Near Infrared Spectroscopy(NIRS)was applied to rapidly assess germplasm variability from whole seed of 699 samples,field-collected and assembled in four genetic and environmentbased sets:one set of 300 varieties of a core-collection and three sets of 133 genotypes of an interspecific population,evaluated in three environments in a large spatial scale of two countries,Mbalmayo and Bafia in Cameroon and Nioro in Senegal,under rainfed conditions.NIR elemental spectra were gathered on six subsets of seeds of each sample,after three rotation scans,with a spectral resolution of 16 cm-1over the spectral range of867 nm to 2530 nm.Spectra were then processed by principal component analysis(PCA)coupled with Partial least squares-discriminant analysis(PLS-DA).As results,a huge variability was found between varieties and genotypes for all NIR wavelength within and between environments.The magnitude of genetic variation was particularly observed at 11 relevant wavelengths such as 1723 nm,usually related to oil content and fatty acid composition.PCA yielded the most chemical attributes in three significant PCs(i.e.,eigenvalues>10),which together captured 93%of the total variation,revealing genetic and environment structure of varieties and genotypes into four clusters,corresponding to the four samples sets.The pattern of genetic variability of the interspecific population covers,remarkably half of spectrum of the core-collection,turning out to be the largest.Interestingly,a PLS-DA model was developed and a strong accuracy of 99.6%was achieved for the four sets,aiming to classify each seed sample according to environment origin.The confusion matrix achieved for the two sets of Bafia and Nioro showed 100%of instances classified correctly with 100%at both sensitivity and specificity,confirming that their seed quality was different from each other and all other samples.Overall,NIRS chemometrics is useful to assess and distinguish seeds from different environments and highlights the value of the interspecific population and core-collection,as a source of nutritional diversity,to support the breeding efforts.

Antioxidant lignans sesamin and sesamolin in sesame(Sesamum indicum L.):a comprehensive review and future prospects

Sesame(Sesamum indicum L.)is a significantly lucrative cash crop for millions of small-holder farmers.Its seeds are an important source of a highly appreciated vegetable oil globally and two clinically essential antioxidant lignans,sesamin and sesamolin.Accordingly,many countries import millions of tons of sesame seed every year.The demand for lignan-rich sesame seeds has been increasing in recent years due to the continuous discovery of several pharmacological attributes of sesamin and sesamolin.To meet this demand,the sesame breeder’s primary objective is to release sesame cultivars that are enriched in oil and lignans.Thus,it is necessary to summarize the information related to the sesamin and sesamolin contents in sesame in order to promote the joint efforts of specialized research teams on this important oilseed crop.In this article,we present the current knowledge on the sesamin and sesamolin contents in S.indicum L.with respect to the updated biosynthesis pathway,associated markers,governing loci,available variability in sesame germplasm,the in planta potential roles of these compounds in sesame,and the newly discovered pharmacological attributes.In addition,we propose and discuss some required studies that might facilitate genomics-assisted breeding of high lignan content sesame varieties.

First Report of a Successful Development of Yam Hybrids(Dioscorea alata L.)from Lyophilized and Long-Term Stored Pollens

Various biological constraints including erratic and asynchronous flowering between male and female plants hinder successful hybrid development and genetic gains in greater yam breeding programs.Therefore,pollen storage has gained much attention to facilitate artificial pollinations and increase the genetic gains.This 4-year study aimed at developing a practical long-term pollen storage technique for the successful development of yam hybrids.Fresh pollens were collected from two Dioscorea alata males,then lyophilized(two lyophilization treatments were applied),followed by storage at room temperature(24℃–25℃)for 12 months.Moreover,the lyophilized and stored pollens were tested for viability by crossing with four female varieties.Our results showed that lyophilization is effective for achieving viable pollens after 12 months of storage.Treatment 1(48 h drying)showed higher pollen germination and fertility rates than Treatment 2(72 h drying).Although we observed a reduction in viability of lyophilized pollens after 12 months of storage,we generated hybrid seedlings with success rates from 12%to 21%compared to 21%–31%when using fresh pollens.Paternity testing based on molecular genotyping confirmed the hybrid status of the obtained seedlings,which grew well in a greenhouse.Lyophilization is a practical approach for a long-term storage of greater yam pollen samples.This protocol will positively impact yam breeding programs particularly in developing countries.

Large scale genetic landscape and population structure of Ethiopian sesame (Sesamum indicum L.) germplasm revealed through molecular marker analysis

Sesame(Sesamum indicum L.) plays a crucial role in Ethiopian agriculture,serving both subsistence and commercial purposes.However,our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited.To address this knowledge gap,we genotyped 368 Ethiopian sesame germplasms,categorizing into four distinct breeding groups:Accessions,landraces,improved varieties,and wild types,using a comprehensive set of 28 polymorphic markers,including 23 simple sequence repeat(SSR) and five Insertion-Deletion(InDel) markers.These markers ensured robust genomic representation,with at least two markers per linkage group.Our results unveiled substantial genetic diversity,identifying a total of 535 alleles across all accessions.On average,each locus displayed 8.83 alleles,with observed and expected heterozygosity values of 0.30 and 0.36,respectively.Gene Diversity and Polymorphic Information Content(PIC) were recorded at 0.37 and 0.35.The percentage of polymorphic loci varied significantly among breeding groups,ranging from8.00% to 82.40%,indicating high diversity in accessions(82.4%),moderate diversity in improved varieties(31.20%) and landraces(29.60%),and limited diversity in wild types(8.00).Analysis of Molecular Variance(AMOVA) results emphasized significant genetic differentiation among populations,with substantial diversity(P<0.001) within each population.Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations,while the larger proportion of genetic diversity(92%) resided within each individual sesame population,showcasing heightened diversity within each group.Our study’s findings received support from both Bayesian clustering and Neighbor-joining(NJ) analysis,reaffirming the credibility of our genetic structure insights.Notably,Population structure analysis at its highest Δk value(k=2) revealed the existence of two primary genetic clusters,further subdivided into four sub-populations at k=4.Similarly,NJ analysis identified two prominent clusters,each displaying additional sub-clustering.In conclusion,our research provides a comprehensive understanding of genetic groups,subpopulations,and overall diversity within Ethiopian sesame populations.These findings underscore the significant genetic diversity and population structure within Ethiopian sesame germplasm collections.This genetic richness holds promise for breeding and conservation efforts,highlighting the importance of preserving genetic diversity to ensure adaptation to changing environments and meet the needs of farmers and consumers.

Genome-wide analysis of the barley non-specific lipid transfer protein gene family

Non-specific lipid transfer proteins(nsLTPs) are small, basic proteins that are characterized by an eight-cysteine motif. The biological functions of these proteins have been reported to involve plant reproduction and biotic or abiotic stress response. With the completion of the barley genome sequence, a genome-wide analysis of nsLTPs in barley(Hordeum vulgare L.)(HvLTPs) will be helpful for understanding the function of nsLTPs in plants. We performed a genome-wide analysis of the nsLTP gene family in barley and identified 70 nsLTP genes,which can be divided into five types(1, 2, C, D, and G). Each type of nsLTPs shares similar exon and intron gene structures. Expression analysis showed that barley nsLTPs have diverse expression patterns, revealing their various roles. Our results shed light on the phylogenetic relationships and potential functions of barley nsLTPs and will be useful for future studies of barley development and molecular breeding.

Multi-scale high-throughput phenotyping of apple architectural and functional traits in orchard reveals genotypic variability under contrasted watering regimes

Despite previous reports on the genotypic variation of architectural and functional traits in fruit trees,phenotyping large populations in the field remains challenging.In this study,we used high-throughput phenotyping methods on an apple tree core-collection(1000 individuals)grown under contrasted watering regimes.First,architectural phenotyping was achieved using T-LiDAR scans for estimating convex and alpha hull volumes and the silhouette to total leaf area ratio(STAR).Second,a semi-empirical index(IPL)was computed from chlorophyll fluorescence measurements,as a proxy for leaf photosynthesis.Last,thermal infrared and multispectral airborne imaging was used for computing canopy temperature variations,water deficit,and vegetation indices.All traits estimated by these methods were compared to low-throughput in planta measurements.Vegetation indices and alpha hull volumes were significantly correlated with tree leaf area and trunk cross sectional area,while IPL values showed strong correlations with photosynthesis measurements collected on an independent leaf dataset.By contrast,correlations between stomatal conductance and canopy temperature estimated from airborne images were lower,emphasizing discrepancies across measurement scales.High heritability values were obtained for almost all the traits except leaf photosynthesis,likely due to large intra-tree variation.Genotypic means were used in a clustering procedure that defined six classes of architectural and functional combinations.Differences between groups showed several combinations between architectural and functional traits,suggesting independent genetic controls.This study demonstrates the feasibility and relevance of combining multi-scale high-throughput methods and paves the way to explore the genetic bases of architectural and functional variations in woody crops in field conditions.

Genome-Wide Association Study of Nitrogen Use Efficiency and Agronomic Traits in Upland Rice

Genome-wide association study(GWAS)was performed for 16 agronomic traits including nitrogen use efficiency(NUE)and yield-related components using a panel of 190 mainly japonica rice varieties and a set of 38390 single nucleotide polymorphism(SNP)markers.This panel was evaluated under rainfed upland conditions in Madagascar in two consecutive cropping seasons with two contrasted nitrogen input levels.Using another set of five grain traits,we identified previously known genes(GW5,GS3,Awn1 and Glabrous1),thus validating the pertinence and accuracy of our datasets for GWAS.A total of 369 significant associations were detected between SNPs and agronomic traits,gathered into 46 distinct haplotype groups and 28 isolated markers.Few association signals were identified for the complex quantitative trait NUE,however,larger number of quantitative trait loci(QTLs)were detected for its component traits,with 10 and 2 association signals for nitrogen utilization efficiency and nitrogen uptake efficiency,respectively.Several detected association signals co-localized with genes involved in nitrogen transport or nitrogen remobilization within 100 kb.The present study thus confirmed the potential of GWAS to identify candidate genes and new loci associated with agronomic traits.However,because of the quantitative and complex nature of NUE-related traits,GWAS might have not captured a large number of QTLs with limited effects.

An integrated approach for increasing breeding efficiency in apple and peach in Europe

Despite the availability of whole genome sequences of apple and peach,there has been a considerable gap between genomics and breeding.To bridge the gap,the European Union funded the FruitBreedomics project(March 2011 to August 2015)involving 28 research institutes and private companies.Three complementary approaches were pursued:(i)tool and software development,(ii)deciphering genetic control of main horticultural traits taking into account allelic diversity and(iii)developing plant materials,tools and methodologies for breeders.Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding,development of new,dense SNP arrays in apple and peach,new phenotypic methods for some complex traits,software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis(PBA).This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies(GWAS)on several European genebank collections.FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities.Through FruitBreedomics,significant progresses were made in the field of apple and peach breeding,genetics,genomics and bioinformatics of which advantage will be made by breeders,germplasm curators and scientists.A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public.This review covers the scientific discoveries made in this major endeavour,and perspective in the apple and peach breeding and genomics in Europe and beyond.

Variability and Synchronism of Leaf Appearance and Leaf Elongation Rates of Eleven Contrasting Rice Genotypes

Leaf appearance and leaf elongation rates in rice play an essential role in determining the development of the plants’ architecture which affects their adaptability to varying environments. This study aimed to characterize the rates of leaf appearance and elongation on all leaves of the main culms of rice plants for 11 contrasting varieties and to determine if the decrease in the leaf appearance rate was related to a simultaneous decrease in the rate of leaf elongation. Forty four 13-L pots were sown with one plant from one genotype and laid out in 4 randomized complete blocks. The experiment, conducted inside a greenhouse, was repeated twice. The increase in length of the leaves expanding on the main stems was monitored daily until flag leaf. Data were used to estimate the rates of leaf appearance and leaf elongation. Significant variability in the rate of leaf appearance, rate of leaf elongation, and leaf length was found across varieties. The kinetics of leaf appearance had linear phases intermediated by a curvilinear phase, without sharp changes in the phyllochron duration. Maximal leaf elongation rate (LER) of all genotypes (except for one) increased linearly with leaf rank until it reached its maximum value at leaf 8 to 10 (11 - 12 for Azucena) where it stabilized before decreasing linearly with leaf rank for the last leaves. Finally, both rates of leaf appearance and leaf elongation evolved with time more smoothly than expected so no sharp decrease in LER occurred at the time of the decrease in leaf appearance rate of the last leaves. However, the trilinear model fits the data well enough to remain useful in efficiently comparing the leaf appearance kinetics of contrasting varieties.

Effect of Proline Pretreatment on Grapevine Shoot-Tip Response to a Droplet-Vitrification Protocol

Proline has been shown to accumulate in plants in response to biotic and abiotic stresses. Exogenous proline has thus been used for improving some plant cryopreservation protocols. Further enhancement of cryopreservation efficiency for in vitro grapevines could be expected if stresses linked to cryopreservation procedures could be reduced. We therefore studied the possible beneficial effect of proline in grapevine cryopreservation. Single-node explants from in vitro grown grapevine plantlets (Vitis vinifera L. cv Portan) were cultured on shooting media (half-strength MS + 1 μM BAP) containing no proline (control) or 50, 500, or 2000 μM filter-sterilized L-proline. Shoot tips excised from these microshoots were subjected to a PVS2-based droplet-vitrification procedure. Control and rewarmed explants were grown on a recovery medium containing 1 μM BAP. Shoot development on control medium and lower proline concentrations did not notably differ whereas the highest concentration of proline inhibited shoot development. Carry-over effects were observed since lower survival and regrowth were obtained both for non-frozen or LN-treated explants excised from micro-shoots obtained on the 2000 μM proline medium. No significant differences in survival and regrowth were observed for non-frozen explants subjected to pretreatment without LN exposure. A slightly enhancing effect (although non-significant) on post-cryopreservation survival was observed for explants derived from shoots developed on 50 or 500 μM proline, but no significant improvement of regrowth percentage was observed for these two conditions. Although a slight increase in survival could be observed, no significant beneficial effect of proline pretreatment on post-cryoconservation regrowth could be evidenced in our conditions. However, the 2-week period before explant excision could have allowed at least partial metabolism and catabolism of exogenous proline;the results observed could thus have been the consequence of complex interactions. Shorter proline treatments applied closer to the actual LN exposure step might produce different results and allow for clearer interpretation.

First characterization of endophytic Corynespora cassiicola isolates with variant cassiicolin genes recovered from rubber trees in Brazil

Corynespora cassiicola is the causal agent of Corynespora Leaf Fall(CLF)disease.CLF is one of the most important fungal diseases of rubber trees in Asia and Africa but disease outbreaks have not been reported in South America.Cassiicolin,a small cysteine-rich glycoprotein secreted by the pathogenic C.cassiicola isolate CCP,was previously identified as a potential disease effector in rubber tree.Recently,the cassiicolin-encoding gene(Cas1)was characterized and shown to be expressed in the early phase of infection.In this study,we investigated whether previously undetected strains of C.cassiicola are present in South American rubber plantations by examining the fungal endophyte population found in asymptomatic rubber tree leaves.Four isolates were identified as C.cassiicola.Genes encoding new forms of the cassiicolin precursor protein(Cas3 and Cas4)were identified from these isolates.Three of four isolates were able to induce symptoms on the cultivar they were isolated from in a detached leaf assay,with different kinetics and intensities.One isolate had the same pathogenicity profile as the pathogenic isolate CCP;the other two isolates developed symptoms late during the course of infection,suggesting saprotrophic capabilities.However,no Cas3 or Cas4 transcripts could be detected upon inoculation with the endophytic isolates,whereas the reference gene Cas1 was expressed upon inoculation with the CCP isolate.This work demonstrated that C.cassiicola is present in South America in an endophytic form and that it may evolve from an endophytic to a saprophytic or even potentially pathogenic life style.

A chromosome-level,haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate wholegenome assembly

Vanilla planifolia, the species cultivated to produce one of the world’s most popular flavors, is highly proneto partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report herethe first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that thediploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequentlyobserved. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gbwith a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequenciesand the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linkinggene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complexmolecular regulation of endoreplication along the chromosomes. This high-quality, anchored assemblyrepresents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidationof this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a userfriendly integrated web portal that enables centralized access to high-throughput genomic and other omicsdata and interoperable use of bioinformatics tools.

XAANTAL2 （AGL14） Is an Important Component of the Complex Gene Regulatory Network that Underlies Arabidopsis Shoot Apical Meristem Transitions

In Arabidopsis thaliana, multiple genes involved in shoot apical meristem （SAM） transitions have been char- acterized, but the mechanisms required for the dynamic attainment of vegetative, inflorescence, and floral meristem （VM, IM, FM） cell fates during SAM transitions are not well understood. Here we show that a MADS-box gene, XAANTAL2 （XAL2/AGL14）, is necessary and sufficient to induce flowering, and its regula- tion is important in FM maintenance and determinacy, xal2 mutants are late flowering, particularly under short-day （SD） condition, while XAL2 overexpressing plants are early flowering, but their flowers have vege- tative traits. Interestingly, inflorescences of the latter plants have higher expression levels of LFY, AP1, and TFL1 than wild-type plants. In addition we found that XAL2 is able to bind the TFL1 regulatory regions. On the other hand, the basipetal carpels of the 35S：：XAL2 lines lose determinacy and maintain high levels of WUS expression under SD condition. To provide a mechanistic explanation for the complex roles of XAL2 in SAM transitions and the apparently paradoxical phenotypes of XAL2 and other MADS-box （SOCl, AGL24） over- expressors, we conducted dynamic gene regulatory network （GRN） and epigenetic landscape modeling. We uncovered a GRN module that underlies VM, IM, and FM gene configurations and transition patterns in wild- type plants as well as loss and gain of function lines characterized here and previously. Our approach thus provides a novel mechanistic framework for understanding the complex basis of SAM development.