Set Of Germplasm Research Articles

Genome-wide association study unravels genomic regions associated with chlorophyll fluorescence parameters in wheat (Triticum aestivum L.) under different sowing conditions.

Genome-wide association study identified 205 significant marker-trait associations for chlorophyll fluorescence parameters in wheat. Candidate gene mining, in silico expression, and promoter analyses revealed the potential candidate genes associated with the studied parameters. The present study investigated the effect of varied sowing conditions (viz., early, timely, and late) on different chlorophyll fluorescence parameters in diverse wheat germplasm set comprising of 198 lines over two cropping seasons (2020-2021 and 2021-2022). Further, a genome-wide association study was conducted to identify potential genomic regions associated with these parameters. The results revealed significant impacts of sowing conditions on all fluorescence parameters, with the maximum and minimum effects on FI (26.64%) and FV/FM (2.12%), respectively. Among the 205 marker-trait associations (MTAs) identified, 11 high-confidence MTAs were chosen, exhibiting substantial effects on multiple fluorescence parameters, and each explaining more than 10% of the phenotypic variation. Through gene mining of genomic regions encompassing high-confidence MTAs, we identified a total of 626 unique gene models. In silico expression analysis revealed 42 genes with an expression value exceeding 2 TPM. Among them, 10 genes were identified as potential candidate genes with functional relevance to enhanced photosynthetic efficiency. These genes mainly encoded for the following important proteins/products-ankyrin repeat protein, 2Fe-2S ferredoxin-type iron-sulfur-binding domain, NADH-ubiquinone reductase complex-1 MLRQ subunit, oxidoreductase FAD/NAD(P)-binding, photosystem-I PsaF, and protein kinases. Promoter analysis revealed the presence of light-responsive (viz., GT1-motif, TCCC-motif, I-box, GT1-motif, TCT-motif, and SP-1) and stress-responsive (viz., ABRE, AuxRR-core, GARE-motif, and ARE) cis-regulatory elements, which may be involved in the regulation of identified putative candidate genes. Findings from this study could directly help wheat breeders in selecting lines with favorable alleles for chlorophyll fluorescence, while the identified markers will facilitate marker-assisted selection of potential genomic regions for improved photosynthesis.

Genomewide selection for fruit quality traits in apple: breeding insights gained from prediction and postdiction.

Many fruit quality traits in apple (Malus domestica Borkh.) are controlled by multiple small-effect quantitative trait loci (QTLs). Genomewide selection (genomic selection) might be an effective breeding approach for highly quantitative traits in woody perennial crops with long generation times like apple. The goal of this study was to determine if genomewide prediction is an effective breeding approach for fruit quality traits in an apple scion breeding program. Representative apple scion breeding germplasm (nindividuals= 955), high-quality single nucleotide polymorphism (SNP) data (nSNPs= 977), and breeding program fruit quality trait data at harvest were analyzed. Breeding parents `Honeycrisp' and `Minneiska' were highly represented. Moderate to high predictive abilities were observed for most fruit quality traits at harvest. For example, when 25% random subsets of the germplasm set were used as training sets, mean predictive abilities ranged from 0.35 to 0.54 across traits. Trait, training and test sets, family size for within family prediction, and number of SNPs per chromosome affected model predictive ability. Inclusion of large-effect QTLs as fixed effects resulted in higher predictive abilities for some traits (e.g. percent red overcolor). Postdiction (i.e. retrospective) analyses demonstrated the impact of culling threshold on selection decisions. The results of this study demonstrate that genomewide selection is a useful breeding approach for certain fruit quality traits in apple.

G×E analysis to Identify the Stable High-yielding Rice Lines among a Set of Selected Germplasm Panel

Rice lines need to be grown and evaluated for yield under different agro-ecological locations to identify stable and high-yielding lines for deployment in breeding programs. With this aim, a set of rice germplasm was evaluated for G×E in four different environments (E1-Dadesuguru-Wet 2020, E2-ICAR–IIRR-Dry 2019, E3-ICAR–IIRR-Wet 2020, E4-ICAR–IIRR-Dry 2020). The experimental trial was laid out in a randomized complete block (RCB) design with three replications at each location for 118 rice lines. Data on yield per plant was analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI) and Genotype, and Genotype × Environment Interaction (GGE) models. The combined analysis of variance (ANOVA) manifested significant variations for tested genotypes, locations, years, genotype × year, and genotype × location interactions revealing the influence of environmental factors on yield traits. All four environments showed discrimination power, whereas E2 and E3 were found as the representative environment as they fall near the Average-Environment axis (AEA). The AMMI biplot PC1 contributed 79.20% variability and PC2 contributed 15.18% variability. From the GGE biplot analysis, the rice lines Phouren, JBB-631-1, and JBB-1325 were found to be the best and most stable. The rice lines Phouren, PUP-229, and TI-112 were stable in the first sub-group Dhadesugur-Wet 2020 (E1). The rice lines Langphou, and NPK-45 were stable in the second sub-group ICAR-IIRR-Wet 2020 (E3). Environment ICAR-IIRR-Dry 2019 (E2) was the third subgroup and the rice lines Moirangphou-Yenthik and TI-3 topped for the same. The ICAR IIRR-Dry 2020 (E4) environment formed the fourth subgroup where Phouren-Amubi, TI-128 and JBB-1325 topped the season. In conclusion, this study revealed that G × E interactions are significant for yield variation, and its AMMI and biplots analysis are efficient tools for visualizing the response of genotypes to different locations.

Genetic Diversity and Population Structure Analysis to Construct a Core Collection from Safflower (Carthamus tinctorius L.) Germplasm through SSR Markers

Genetic resources are the fundamental source of diversity available to plant breeders for the improvement of desired traits. However, a large germplasm set is difficult to preserve and use as a working collection in genetic studies. Hence, the present study evaluates the genetic diversity of 3115 safflower accessions from the Indian National Gene Bank, including Indian cultivars, to develop a manageable set of accessions, with similar genetic variations of germplasm studied. A total of 18 polymorphic SSR markers were used. The genetic diversity analysis revealed that germplasm accessions were highly diverse and there is no correlation between genetic diversity and the geographical collection of germplasm or sourcing of germplasm. A core set was developed using a core hunter software with different levels of composition, and it was found that 10% of the accessions showed maximum gene diversity and represented an equal number of alleles and major allele frequency in the germplasm studied. The developed core consisted of 351 accessions, including Indian cultivars, and they were validated with various genetic parameters to ascertain that they were a true core set for the studied accessions of safflower germplasm.

Identification of multiple abiotic stress tolerant donors for climate-resilient rice (Oryza sativa) development

The increasing occurrence of adverse weather events is continuously challenging agricultural production globally. The wide genetic base of rice (Oryza sativa L.) and the availability of a diverse set of germplasm can be explored to identify multiple abiotic stress-tolerant donors for rice improvement. Therefore, an experiment was conducted during 2018–21 at ICAR-National Rice Research Institute, Cuttack, Odisha to evaluate diverse rice germplasm (68 accessions) for vegetative stage drought and submergence stress and for their anaerobic germination potential. Under drought stress, 49 accessions showed a drought score (DS) of 1 indicating a tolerance response. The early vegetative score indicated that 58 accessions were highly vigorous, while the drought recovery score indicates that >90% of the genotypes showed good recovery after the drought cycle. The same genotypes showed a average survival rate (SR) of 48% under two weeks of complete submergence. Among them, 11 were found highly tolerant with >70% SR and 26 genotypes scored positive SUB1A locus by SNP-based functional marker AEX1. Nearly 50% of the genotypes scored positive for SUB1A, based on both AEX1 and Sub1A203 markers, which nearly matched the phenotyping result. Out of 68, only 4 accessions showed more than 50% germination under anaerobic conditions. A multivariate analysis showed that 11 genotypes had both drought and submergence tolerance, while 6 genotypes were having tolerance to drought and anaerobic germination. We found only 1 accession (IC516149) tolerant to all these 3 stresses which can be identified as a potential donor for multiple abiotic stresses.

Haplotype Analysis Sheds Light on the Genetic Evolution of the Powdery Mildew Resistance Locus Pm60 in Triticum Species.

Wheat powdery mildew (Blumeria graminis f. sp. tritici, Bgt, recently clarified as B. graminis s. str.), is one of the most destructive diseases of wheat. Pm60 is a nucleotide-binding leucine-rich repeat (NLR) gene that confers race-specific resistance to Bgt. Allelic variants (Pm60, Pm60a, and Pm60b) were found in Triticum urartu and T. dicoccoides, the wild progenitors of wheat. In the present study, we studied the diversity of the Pm60 locus in a large set of wheat germplasm and found 20 tetraploid wheats harboring the Pm60 alleles, which correspond to three novel haplotypes (HapI-HapIII). HapI (Pm60 allele) and HapII (Pm60a allele) were present in domesticated tetraploid wheats, whereas HapIII (Pm60a allele) was identified in wild tetraploid T. araraticum. A sequence comparison of HapII and HapIII revealed that they differed by three SNPs and a GCC deletion. Results of the phylogenetic analysis revealed that HapII was more closely related to the functional haplotype MlIW172. Infection tests showed that HapII-carrying lines display a partial resistance response to Bgt#GH, while HapI was susceptible. Our results provide insights into the genetic evolution of the Pm60 locus and potential valuable alleles for powdery mildew resistance breeding.

Identification of waxy genotype in sorghum genetic resources using waxy gene-based markers and iodine staining methods

Sorghum is widely recognized as a versatile crop with significant value in the production of food and energy. Sorghum with waxy trait (low amylose) is more palatable to the food industries and more appealing to consumers than nonwaxy variety. However, waxy sorghum has not yet been introduced to Indonesia, making it difficult to use sorghum to support the government of Indonesia's initiative to diversify the country's main foods. This study aimed at identify the waxy traits in a set of sorghum germplasm collected in Indonesia using waxy gene-based markers and iodine staining screening approaches. A total of 48 (27 introduced and 21 local) sorghum accessions collected in the IAARD gene bank along with 4 national sorghum varieties, which were subjected to both molecular analysis and iodine staining assay. The presence of waxy allele in the sorghum gene bank collection was identified using DNA markers associated with two waxy alleles (wxa and wxc). Iodine staining assay performed in the present study was applied to verify the waxy phenotype in sorghum grain and waxy genotypes in sorghum pollen. Based on molecular analysis and pollen staining, five local sorghum accessions were classified as heterowaxy sorghum. These accessions showed reddish-brown color in their endosperm after treated by iodine staining which confirmed them as waxy phenotype. These findings would be beneficial for further improvement of grain quality in sorghum breeding programs

Association mapping for broomrape resistance in sunflower.

Sunflower breeding for resistance to the parasitic plant sunflower broomrape (Orobanche cumana Wallr.) requires the identification of novel resistance genes. In this research, we conducted a genome-wide association study (GWAS) to identify QTLs associated with broomrape resistance. The marker-trait associations were examined across a germplasm set composed of 104 sunflower accessions. They were genotyped with a 600k AXIOM® genome-wide array and evaluated for resistance to three populations of the parasite with varying levels of virulence (races EFR, FGV, and GTK) in two environments. The analysis of the genetic structure of the germplasm set revealed the presence of two main groups. The application of optimized treatments based on the general linear model (GLM) and the mixed linear model (MLM) allowed the detection of 14 SNP markers significantly associated with broomrape resistance. The highest number of marker-trait associations were identified on chromosome 3, clustered in two different genomic regions of this chromosome. Other associations were identified on chromosomes 5, 10, 13, and 16. Candidate genes for the main genomic regions associated with broomrape resistance were studied and discussed. Particularly, two significant SNPs on chromosome 3 associated with races EFR and FGV were found at two tightly linked SWEET sugar transporter genes. The results of this study have confirmed the role of some QTL on resistance to sunflower broomrape and have revealed new ones that may play an important role in the development of durable resistance to this parasitic weed in sunflower.

Thiamine improves in vitro propagation of sweetpotato [Ipomoea batatas (L.) Lam.] – confirmed with a wide range of genotypes

In vitro propagation of Plant Genetic Resources is a basic step for routine genebank and biotechnology research activities. Accelerating growth and rooting of in vitro plants contributes to an improvement in process efficiency and plant quality. In the present study the effect of supplemental thiamine and explant size on biometric variables, ion content in plant sap, chlorophyll content in leaves and moisture content in plants were assessed in a replicated trial on a group of seven in vitro sweetpotato accessions and validated in a set of other 45 accessions. It was shown that adding 0.1 mg L −1 of thiamine to modified Murashige and Skoog culture medium significantly increased plant height, root length, and number of nodes of in vitro sweetpotato shoot culture plants. No significant differences were observed for N03−, K+, Na+ and Ca++—ion content in plant sap, nor in leaf area, chlorophyll, or moisture content between plants grown with or without thiamine. Uninodal stem segments showed on thiamine-free medium a significantly lower root and plant growth, and reduced number of nodes, than plants grown from uni- and binodal segments on thiamine-supplemented medium. A subsequent experiment tested all the parameters above in a non-replicated screen with a set of 45 diverse sweetpotato accessions. With this diverse set of germplasm, the average plant and root length increased by 41 and 51%, respectively on thiamine-supplemented culture medium compared to the control treatment, confirming that supplemental thiamine is generally beneficial to sweetpotato in vitro shoot culture.

Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation

Key messageStructural variants (SV) of 23 barley inbreds, detected by the best combination of SV callers based on short-read sequencing, were associated with genome-wide and gene-specific gene expression and, thus, were evaluated to predict agronomic traits.In human genetics, several studies have shown that phenotypic variation is more likely to be caused by structural variants (SV) than by single nucleotide variants. However, accurate while cost-efficient discovery of SV in complex genomes remains challenging. The objectives of our study were to (i) facilitate SV discovery studies by benchmarking SV callers and their combinations with respect to their sensitivity and precision to detect SV in the barley genome, (ii) characterize the occurrence and distribution of SV clusters in the genomes of 23 barley inbreds that are the parents of a unique resource for mapping quantitative traits, the double round robin population, (iii) quantify the association of SV clusters with transcript abundance, and (iv) evaluate the use of SV clusters for the prediction of phenotypic traits. In our computer simulations based on a sequencing coverage of 25x, a sensitivity > 70% and precision > 95% was observed for all combinations of SV types and SV length categories if the best combination of SV callers was used. We observed a significant (P < 0.05) association of gene-associated SV clusters with global gene-specific gene expression. Furthermore, about 9% of all SV clusters that were within 5 kb of a gene were significantly (P < 0.05) associated with the gene expression of the corresponding gene. The prediction ability of SV clusters was higher compared to that of single-nucleotide polymorphisms from an array across the seven studied phenotypic traits. These findings suggest the usefulness of exploiting SV information when fine mapping and cloning the causal genes underlying quantitative traits as well as the high potential of using SV clusters for the prediction of phenotypes in diverse germplasm sets.

Genotypic variation of yield-related traits in an irrigated rice breeding program for tropical Asia

Developing high-yielding rice varieties is critical to ensure global food security. To date, selection of promising genotypes is based on empirical evaluation for grain yield, but the relationship of agronomic traits to yield in tropical rice breeding is largely unknown. This study aimed to determine the extent of variation for 19 agronomic traits and interrelationships among traits in an irrigated rice breeding program at the International Rice Research Institute, Philippines. A large set of elite germplasm comprising advanced genotypes and varieties derived from the breeding pipeline was evaluated during dry and wet seasons. The broad-sense heritability ranged from 0.35 to 0.99 for all traits in both seasons. Grain yield for the whole plot (plot yield) was positively correlated with yield per plant, 1000 grain weight, and grain width in dry season, and yield per plant, 1000 grain weight, grain width, number of panicles per plant, and panicle exertion rate in wet season. Path analysis showed that the highest direct positive effect of traits on plot yield ranged from 0.25 to 0.45 in dry season and from 0.22 to 0.88 in wet season. Heat map bi-cluster analysis assigned genotypes into three main clusters in both seasons, while traits were grouped into three and five clusters in dry and wet seasons, respectively. The cluster analysis showed that spikelets per panicle, filled grains per plant, and yield per plant were key yield contributing traits. Identification of traits that were highly correlated with rice yield could be useful for developing new varieties adapted to tropical environments.

Genetic networks underlying salinity tolerance in wheat uncovered with genome-wide analyses and selective sweeps.

A genetic framework underpinning salinity tolerance at reproductive stage was revealed by genome-wide SNP markers and major adaptability genes in synthetic-derived wheats, and trait-associated loci were used to predict phenotypes. Using wild relatives of crops to identify genes related to improved productivity and resilience to climate extremes is a prioritized area of crop genetic improvement. High salinity is a widespread crop production constraint, and development of salt-tolerant cultivars is a sustainable solution. We evaluated a panel of 294 wheat accessions comprising synthetic-derived wheat lines (SYN-DERs) and modern bread wheat advanced lines under control and high salinity conditions at two locations. The GWAS analysis revealed a quantitative genetic framework of more than 200 loci with minor effect underlying salinity tolerance at reproductive stage. The significant trait-associated SNPs were used to predict phenotypes using a GBLUP model, and the prediction accuracy (r2) ranged between 0.57 and 0.74. The r2 values for flag leaf weight, days to flowering, biomass, and number of spikes per plant were all above 0.70, validating the phenotypic effects of the loci discovered in this study. Furthermore, the germplasm sets were compared to identify selection sweeps associated with salt tolerance loci in SYN-DERs. Six loci associated with salinity tolerance were found to be differentially selected in the SYN-DERs (12.4Mb on chromosome (chr)1B, 7.1Mb on chr2A, 11.2Mb on chr2D, 200Mb on chr3D, 600Mb on chr6B, and 700.9Mb on chr7B). A total of 228 reported markers and genes, including 17 well-characterized genes, were uncovered using GWAS and EigenGWAS. A linkage disequilibrium (LD) block on chr5A, including the Vrn-A1 gene at 575Mb and its homeologs on chr5D, were strongly associated with multiple yield-related traits and flowering time under salinity stress conditions. The diversity panel was screened with more than 68 kompetitive allele-specific PCR (KASP) markers of functional genes in wheat, and the pleiotropic effects of superior alleles of Rht-1, TaGASR-A1, and TaCwi-A1 were revealed under salinity stress. To effectively utilize the extensive genetic information obtained from the GWAS analysis, a genetic interaction network was constructed to reveal correlations among the investigated traits. The genetic network data combined with GWAS, selective sweeps, and the functional gene survey provided a quantitative genetic framework for identifying differentially retained loci associated with salinity tolerance in wheat.

Large-Effect QTLs for Titratable Acidity and Soluble Solids Content Validated in ‘Honeycrisp’-Derived Apple Germplasm

Fruit acidity and sweetness are important fruit quality traits in the apple and are therefore targets in apple breeding programs. Multiple quantitative trait loci (QTLs) associated with titratable acidity (TA) and soluble solids content (SSC) have been previously detected. In this study a pedigree-based QTL analysis approach was used to validate QTLs associated with TA and SSC in a ‘Honeycrisp’-derived germplasm set. TA and SSC data collected from 2014 to 2018 and curated genome-wide single nucleotide polymorphism (SNP) data were leveraged to validate three TA QTLs on linkage groups (LGs) 1, 8, and 16 and three SSC QTLs on LGs 1, 13, and 16. TA and SSC QTL haplotypes were characterized in six University of Minnesota apple breeding families representing eight breeding parents including ‘Honeycrisp’ and ‘Minneiska’. Six high-TA haplotypes, four low-TA haplotypes, 14 high-SSC haplotypes, and eight low-SSC haplotypes were characterized. The results of this study will enable more informed selection in apple breeding programs.

Genetic Diversity and Population Structure of Schima superba From Southern China

The tree Schima superba is important for afforestation and fire prevention in southern China. The wood of this tree can also be used for furniture and buildings. However, the lack of genetic background and genomic information for this species has lowered wood yield speed and quality improvement. Here, we aimed to discover genome-wide single nucleotide polymorphisms (SNPs) in 302 S. superba germplasms collected from southern China and to use these SNPs to investigate the population structure. Using genotyping by sequencing, a total of 785 high-quality SNP markers (minor allele frequency [MAF] ≥ 0.05) were identified from 302 accessions collected from seven geographical locations. Population structure analyses and principal coordinate analyses (PCoAs) indicated that these germplasm resources can be clearly separated into different populations. The S. superba accessions originating from Yunnan (YN) and Guangxi (GX) fell into the same population, separate from the accessions originating from Guangdong (GD), which indicated that these two regions should be regarded as major provenances of this species. In addition, two independent core germplasm sets with abundant genetic polymorphisms were constructed to support the breeding work. The identification of SNP markers, analyses of population genetics, and construction of core germplasm sets will greatly promote the molecular breeding work of S. superba.

Fall Armyworm Tolerance of Maize Parental Lines, Experimental Hybrids, and Commercial Cultivars in Southern Africa

Fall armyworm [Spodoptera frugiperda (J./E. Smith); FAW] is negatively impacting sustainable maize production, particularly in smallholder farming systems in sub-Saharan Africa. Two sets of germplasm (commercial cultivars and experimental hybrids, and local and exotic inbred lines) were evaluated under managed and natural FAW infestation to identify FAW tolerant material with superior grain yield performance. Significant genotypic effects on foliar FAW damage, ear FAW damage, and grain yield were observed. Commercial cultivars were significantly more affected by FAW infestation than experimental hybrids, as evidenced by high foliar and ear damage scores, yet they out-yielded experimental genotypes. The introduced FAW donor lines (CML338, CML67, CML121, and CML334) showed better tolerance to FAW, individually and in hybrid combinations. Local inbred lines, SV1P, CML491, and CML 539, also showed FAW tolerance. Hybrids and open pollinated varieties were more vulnerable to FAW damage at early growth stages, but they grew out of it through the mid to late whorl stages. Inbred lines showed increasing damage as they grew to maturity. Husk cover, ear rot, anthesis date, and plant height were highly correlated with FAW tolerance. The identified local and exotic lines with FAW tolerance will contribute to FAW resistance breeding in southern Africa.

GENETIC DIVERSITY ANALYSIS OF COMMON BEAN (PHASEOLUS VULGARIS L.) GENOTYPES USING SCOT POLYMORPHISM

Common bean (Phaseolus vulgaris L.) is legume crop of worldwide importance and due to optimal content of proteins and other essential compounds it has a potential as a functional food. Genetic diversity studies are significant from the point of obtaining information important for breeding process. The goal of present work was to analyze genetic diversity among 34 genotypes of common bean from different countries using 5 SCoT (Start Codon Targeted) markers. Altogether 82 DNA fragments were amplified, out of which 66 fragments were polymorphic with an average of 11 polymorphic fragments per primer. The highest number of polymorphic fragments was detected by marker SCoT 59 (15). The percentage of polymorphism ranged from 57.17% (SCoT 2) to 78.57% (SCoT 19) with an average of 67.3%. PIC values varied from 0.719 (SCoT 19) to 0.886 (SCoT 3) and average PIC value was 0.802. The DI values varied between 0.722 (SCoT 19) and 0.888 (SCoT3), with an average of 0.804. The dendrogram of 34 genotypes of common bean, constructed based on hierarchical cluster analysis separated genotypes into two clusters (I and II). Cluster I was formed by two subclusters. Thirty-three genotypes were included in cluster I and genotype Albena (Slovak Republic), which significantly differed from other genotypes in seed size was included in cluster II. Obtained results support the effectiveness of SCoT markers in the analysis of common bean useful for genotypes differentiating and assessment of genetic diversity in the set of common bean germplasm.

The World Vegetable Center Amaranthus germplasm collection: Core collection development and evaluation of agronomic and nutritional traits

AbstractAmaranth (Amaranthus spp.) is an underutilized crop increasing in popularity as a grain and as a leafy vegetable. It is rich in protein, minerals, and vitamins, and adapts well to a range of production systems. Currently, the lack of improved cultivars limits the use of the crop. Breeding‐improved cultivars requires access to large collections of amaranth biodiversity stored in genebanks. The task of searching such vast collections for traits of interest can be eased by generating core collections, which display the diversity of large collections in a much smaller germplasm set. The World Vegetable Center amaranth collection contains around 1,000 accessions of 13 species; among them, there are 281 accessions of four species important for use as vegetable amaranth in Africa (A. cruentus, A. hypochondriacus, A. caudatus, and A. dubius). Based on single nucleotide polymorphism (SNP) marker genotype diversity, a core collection (CC) of 76 accessions, cultivars, and selections was assembled. To a large extent, it represents the diversity of the whole collection. The CC was evaluated for yield and nutritional parameters during the cool and warm seasons in Tanzania and Taiwan and a pretest for variation of drought tolerance in the CC has been performed. Cultivar Madiira 2, an improved cultivar developed for vegetable production in Africa, outperformed all other tested cultivars in terms of yield stability, but several CC accessions had higher yield, lower wilting score, and higher nutrient content than Madiira 2. This indicates the core collection can be used for further improvement of amaranth cultivars.

AFLP-based assessment of genetic variation in certain Indian elite cultivars of Cymbopogon species

Cymbopogon, one of the major aromatic genera of Poaceae family, is mainly cultivated for its essential oils that hold promising medicinal and commercial value. In India, several improved cultivars of Cymbopogon species are developed for commercial cultivation and conceded by means of agronomic and chemotypic traits. Information on genetic variability in these commercial cultivars is still limited which poses a problem in further improvement of oil grasses. The present study aimed to investigate the genetic variation among certain improved Indian cultivars of three commercially important Cymbopogon sp. i.e., C. flexuosus, C. winterianus and C. martinii using amplified fragment length polymorphism (AFLP) markers. A total of 94 robust loci were amplified using 8 AFLP primer combinations. Among the total amplified fragments, 72 were polymorphic which showed 76.59% polymorphism across all the germplasm. Polymorphic information content (PIC) and marker index (MI) values showed significant positive correlation (r2 =0.936, p < 0.005) in determining the discriminatory power of the AFLP primer combinations. A higher effective multiplex ratio (EMR) and MI values were recorded for the primer combinations that generated higher polymorphism across the genotypes. To obtain the genetic information at the intra- and inter species level, genetic diversity indices were calculated. Genetic heterogeneity was noticed in the order C. martinii>C. flexuosus>C. winterianus. UPGMA-phenogram and principal coordinate analysis (PCA) separated all the cultivars as per the chemotaxonomic series with a few exceptions. Molecular diversity explained and diagnostic fragments developed through AFLP markers in this study could provide a detailed cataloguing of Cymbopogon cultivars for genetic conservation purpose and also useful for exploration and improvement of diverse set of germplasm.

Meta-QTLs linked to nitrogen use efficiency are randomly distributed in Indian rice germplasm

Nitrogen (N) recognized as a critical element for plant growth plays a fundamental role in rice cultivation. The N use efficiency (NUE) hovers around 30-35% in rice, suggesting a significant loss of N from the rice fields. Improving the NUE therefore would require genetic interventions and breeding. The cultivar improvement for N uptake and utilization is required to elevate NUE to further heights. Several quantitative trait loci (QTLs) for NUE under varying conditions and genetic backgrounds have been reported in rice. Consolidation of this distributed and unorganized information is necessary to identify critical genomic regions to be used for crop improvement. Therefore, a Meta-analysis from an assembly of 506 QTLs reported from 18 different studies was performed to identify the most significant genomic regions associated with NUE in rice. A total of 12 meta-QTLs (mQTLs) related to the traits such as NUE and grain yield per plant under N deficit conditions have been identified over four rice chromosomes namely 1, 3, 4, and 8. Evaluation of these mQTLs in a set of Indian rice germplasm revealed a significant association of the meta loci with N use parameters and showed wide distribution in the germplasm. Identification of mQTLs on different chromosomes together with their respective markers will help recruit them in marker-assisted selection (MAS) to develop N use efficient genotypes.

Identification of novel resources for panicle blast resistance from wild rice accessions and mutants of cv. Nagina 22 by syringe inoculation under field conditions.

Panicle blast is the most severe type of rice blast disease. Screening of rice genotypes for panicle blast resistance at the field level requires an efficient and robust method of inoculation. Here, we standardized a method that can be utilized for both small- and large-scale screening and assessment of panicle blast infection and disease reaction. The method involves inoculation of Magnaporthe oryzae spore culture in the neck of the rice panicle using a syringe and covering the inoculation site with wet cotton wrapped with aluminum foil to provide the required humidity for spore germination. The method was standardized using panicle blast-resistant cv. Tetep and susceptible cv. HP2216 inoculated with Mo-ni-025 isolate of M. oryzae. The method was evaluated at phenotypic as well as molecular level by expression analysis of disease responsive pathogenesis-related (PR) genes. We found this method simple, robust, reliable, and highly efficient for screening of large germplasm sets of rice for panicle blast. This was validated by screening the wild rice germplasm for panicle blast response in the field using three M. oryzae strains and subsequently with the most virulent strain in 45 EMS-induced mutants of Nagina 22 shortlisted based on field screening in a blast hotspot region. We identified five novel blast disease-resistant wild rice genotypes and 15 Nagina 22 mutants that can be used in breeding programmes.