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Broomcorn millet (Panicum miliaceum L.) is a crop with a good ability to adapt to the environment. Over 8800 accessions have been collected in the national gene bank of China. The huge quantity of germplasms made it difficult for analysis and evaluation. Although a broomcorn millet core collection (CC) comprising 780 accessions was established, the number is still too large for researchers to explore in depth. In this study, the genetic diversity of 634 broomcorn millet accessions from the core collection was analyzed based on SSR markers. A mini-core collection (MC) containing 256 accessions was extracted. The mini-core collection accounted for less than half of the original core collection and only about 2.8% of the total resources but still provided a good representation. In addition, the results of this study validated that Shanxi is the origin of broomcorn millet, and accessions from the South region may contain novel genes. In conclusion, this study provides a comprehensive characterization of the genetic diversities of broomcorn millet core collection in China. Moreover, an MC may aid in reasonably and efficiently selecting materials for broomcorn millet breeding as researchers could screen for aimed genetic characters within a smaller scope. [ABSTRACT FROM AUTHOR]

Sorghum (Sorghum bicolor L.) ranks fifth as the most crucial cereal crop globally, yet its seed morphology remains relatively unexplored. This study investigated seed morphology in sorghum based on 115 mini-core and 130 Senegalese germplasms. Eight seed morphology traits encompassing size, shape, and color parameters were assessed. Statistical analyses explored potential associations between these traits and resistance to three major sorghum diseases: anthracnose, head smut, and downy mildew. Furthermore, genome-wide association studies (GWAS) were conducted using phenotypic data from over 24,000 seeds and over 290,000 publicly available single nucleotide polymorphisms (SNPs) through the Genome Association and Prediction Integrated Tool (GAPIT) R package. Significant SNPs associated with various seed morphology traits were identified and mapped onto the reference sorghum genome to identify novel candidate defense genes. [ABSTRACT FROM AUTHOR]

Sorghum (Sorghum bicolor L.) ranks fifth as the most crucial cereal crop globally, yet its seed morphology remains relatively unexplored. This study investigated seed morphology in sorghum based on 115 mini-core and 130 Senegalese germplasms. Eight seed morphology traits encompassing size, shape, and color parameters were assessed. Statistical analyses explored potential associations between these traits and resistance to three major sorghum diseases: anthracnose, head smut, and downy mildew. Furthermore, genome-wide association studies (GWAS) were conducted using phenotypic data from over 24,000 seeds and over 290,000 publicly available single nucleotide polymorphisms (SNPs) through the Genome Association and Prediction Integrated Tool (GAPIT) R package. Significant SNPs associated with various seed morphology traits were identified and mapped onto the reference sorghum genome to identify novel candidate defense genes.

Enhancing the root traits through selection and breeding efforts can significantly improve the acquisition of soil resources, consequently boosting crop production in marginal environments. Cowpea is one of the important legume crops in arid and semi-arid regions, grown mostly in marginal environments under drought conditions. The roots play a crucial role in plant's ability to survive and adapt under such water stressed conditions. The understanding of cowpea genetic architecture related to root system architecture (RSA) remains limited due to difficulties in accurately measuring root traits. In the present study, a set 110 diverse mini-core collection of cowpea from IITA, Nigeria was evaluated for thirteen (13) different root-shoot traits under controlled conditions in the green house. Significant variation was recorded for all the root traits in the mini-core set. Most promising genotype for most of the root traits, viz., root volume, dry root weight, root biomass density and tap root diameter were identified. The correlation analysis revealed significant positive association (p < 0.001) of root weight with shoot weight (0.85), root volume (r = 0.61), and tap root diameter (0.56). In the principal component analysis (PCA), first three principal components explained the variance of 64.31%, with PC1 contributing 44.43%, PC2 10% and PC3 9.88%. All the root-shoot traits contribute positive variation to PC1especially dry root weight and dry shoot weight that had high component loading and in PC2 root shoot ratio had high loading. The root-shoot trait data was used with 6,574 good quality SNP data for discovery of genes/QTLs/marker-trait associations for root traits. The analysis of results of genome wide association study (GWAS) led to the identification of 52 unique SNPs associated significantly (p < 10−4) with thirteen root-shoot traits. Highest number of SNPs was found associated with root weight and chromosome 5 was identified as SNP hotspot for harboring majority of significant SNPs. We further delve candidate genes within 50 kb around the identified SNP that led to the identification of several important candidate genes underlying genomic regions responsible for root-shoot traits in cowpea. The promising cowpea genotypes for root traits and promising MTAs/candidate genes will prove useful in cowpea improvement programs including improvement of drought tolerance in cowpea.

Broomcorn millet (Panicum miliaceum L.) is a crop with a good ability to adapt to the environment. Over 8800 accessions have been collected in the national gene bank of China. The huge quantity of germplasms made it difficult for analysis and evaluation. Although a broomcorn millet core collection (CC) comprising 780 accessions was established, the number is still too large for researchers to explore in depth. In this study, the genetic diversity of 634 broomcorn millet accessions from the core collection was analyzed based on SSR markers. A mini-core collection (MC) containing 256 accessions was extracted. The mini-core collection accounted for less than half of the original core collection and only about 2.8% of the total resources but still provided a good representation. In addition, the results of this study validated that Shanxi is the origin of broomcorn millet, and accessions from the South region may contain novel genes. In conclusion, this study provides a comprehensive characterization of the genetic diversities of broomcorn millet core collection in China. Moreover, an MC may aid in reasonably and efficiently selecting materials for broomcorn millet breeding as researchers could screen for aimed genetic characters within a smaller scope.

Objective: To understand the geographic differences and variations in the functional components of brown rice cores collected from global rice germplasms. Methods: Four functional components, γ-aminobutyric acid (GABA), resistant starch (RS), total flavonoids, and alkaloids, in brown rice from 690 mini-core collections from 31 countries from five continents and the International Rice Research Institute, were analyzed using a spectrophotometry colorimetric method, and the results were statistically validated. Conclusion: The highest average amounts of functional components were obtained in Asian germplasms, except for GABA, and total flavonoids were highest in brown rice from Europe and Oceania, followed by Asia. The highest coefficient of variation for GABA was observed in Asia; that for RS and total flavonoids was observed in Africa, followed by Asia; and that for alkaloids was observed in America, followed by Asia. Overall, Asian countries were the most prominent and representative zones with the highest genotypic potential for functional components of brown rice. Forty-one rice accessions with enriched functional components originated mostly from biodiversity-rich areas in China, followed by those in the Philippines. Late sowing favored the enrichment of these components in brown rice. The current study provides a reference for rice breeding with enriched functional constituents, and guidelines for screening functional rice that could be used for human chronic disease research.

The highly diverse Colombian Central Collection (CCC) of cultivated potatoes is the most important source of genetic variation for breeding and the agricultural development of this staple crop in Colombia. Potato is the primary source of income for more than 100.000 farming families in Colombia. However, biotic and abiotic challenges limit crop production. Furthermore, climate change, food security, and malnutrition constraints call for adaptive crop development to be urgently addressed. The clonal CCC of potatoes contains 1,255 accessions - an extensive collection size that limits its optimal assessment and use. Our study evaluated different collection sizes from the whole clonal collection to define the best core collection that captures the total genetic diversity of this unique collection, to support a characterization more cost-effectively. Initially, we genotyped 1,141 accessions from the clonal collection and 20 breeding lines using 3,586 genome-wide polymorphic markers to study CCC’s genetic diversity. The analysis of molecular variance confirmed the CCC’s diversity with a significant population structure (Phi=0.359; p-value=0.001). Three main genetic pools were identified within this collection (CCC_Group_A, CCC_Group_B1, and CCC_Group_B2), and the commercial varieties were located across the pools. The ploidy level was the main driver of pool identification, followed by a robust representation of accessions from Phureja and Andigenum cultivar groups based on former taxonomic classifications. We also found divergent heterozygosity values within genetic groups, with greater diversity in genetic groups with tetraploids (CCC_Group_B1: 0.37, and CCC_Group_B2: 0.53) than in diploid accessions (CCC_Group_A: 0.14). We subsequently generated one mini-core collection size of 3 percent (39 entries) and three further core collections sizes of 10, 15, and 20 percent (i.e., 129, 194, and 258 entries, respectively) from the total samples genotyped. As our results indicated that genetic diversity was similar across the sampled core collection sizes compared to the main collection, we selected the smallest core collection size of 10 percent. We expect this 10 percent core collection to be an optimal tool for discovering and evaluating functional diversity in the genebank to advance potato breeding and agricultural-related studies. This study also lays the foundations for continued CCC curation by evaluating duplicity and admixing between accessions, completing the digitalization of data, and ploidy determination using chloroplast count. [ABSTRACT FROM AUTHOR]

The highly diverse Colombian Central Collection (CCC) of cultivated potatoes is the most important source of genetic variation for breeding and the agricultural development of this staple crop in Colombia. Potato is the primary source of income for more than 100.000 farming families in Colombia. However, biotic and abiotic challenges limit crop production. Furthermore, climate change, food security, and malnutrition constraints call for adaptive crop development to be urgently addressed. The clonal CCC of potatoes contains 1,255 accessions ― an extensive collection size that limits its optimal assessment and use. Our study evaluated different collection sizes from the whole clonal collection to define the best core collection that captures the total genetic diversity of this unique collection, to support a characterization more cost-effectively. Initially, we genotyped 1,141 accessions from the clonal collection and 20 breeding lines using 3,586 genome-wide polymorphic markers to study CCC’s genetic diversity. The analysis of molecular variance confirmed the CCC’s diversity with a significant population structure (Phi=0.359; p-value=0.001). Three main genetic pools were identified within this collection (CCC_Group_A, CCC_Group_B1, and CCC_Group_B2), and the commercial varieties were located across the pools. The ploidy level was the main driver of pool identification, followed by a robust representation of accessions from Phureja and Andigenum cultivar groups based on former taxonomic classifications. We also found divergent heterozygosity values within genetic groups, with greater diversity in genetic groups with tetraploids (CCC_Group_B1: 0.37, and CCC_Group_B2: 0.53) than in diploid accessions (CCC_Group_A: 0.14). We subsequently generated one mini-core collection size of 3 percent (39 entries) and three further core collections sizes of 10, 15, and 20 percent (i.e., 129, 194, and 258 entries, respectively) from the total samples genotyped. As our results indicated that genetic diversity was similar across the sampled core collection sizes compared to the main collection, we selected the smallest core collection size of 10 percent. We expect this 10 percent core collection to be an optimal tool for discovering and evaluating functional diversity in the genebank to advance potato breeding and agricultural-related studies. This study also lays the foundations for continued CCC curation by evaluating duplicity and admixing between accessions, completing the digitalization of data, and ploidy determination using chloroplast count.

Diversity surveys of crop germplasm are important for gaining insights into the genomic basis for plant architecture and grain yield improvement, which is still poorly understood in wheat. In this study, we exome sequenced 287 wheat accessions that were collected in the past 100 years. Population genetics analysis identified that 6.7% of the wheat genome falls within the selective sweeps between landraces and cultivars, which harbors the genes known for yield improvement. These regions were asymmetrically distributed on the A and B subgenomes with regulatory genes being favorably selected. Genome-wide association study (GWAS) identified genomic loci associated with traits for yield potential, and two underlying genes, TaARF12 encoding an auxin response factor and TaDEP1 encoding the G-protein γ-subunit, were located and characterized to pleiotropically regulate both plant height and grain weight. Elite single-nucleotide haplotypes with increased allele frequency in cultivars relative to the landraces were identified and found to have accumulated over the course of breeding. Interestingly, we found that TaARF12 and TaDEP1 function in epistasis with the classical plant height Rht-1 locus, leading to propose a "Green Revolution"-based working model for historical wheat breeding. Collectively, our study identifies selection signatures that fine-tune the gibberellin pathway during modern wheat breeding and provides a wealth of genomic diversity resources for the wheat research community. Exome sequencing of 287 wheat accessions representing a collection from the past 100 years in China and genome-wide association study identified epistatically interacting pleiotropic genomic loci for yield potential. Selection signatures identified suggest that the gibberellin pathway is fine-tuned in post-Green Revolution breeding efforts. This rich genomic diversity resource will be useful for the wheat research community. [ABSTRACT FROM AUTHOR]

Peanut is an important legume crop worldwide. To uncover the genetic basis of yield features and assist breeding in the future, we conducted genome-wide association studies (GWAS) for six yield-related traits of the Chinese peanut mini-core collection. The seed (pod) size and weight of the population were investigated under four different environments, and these traits showed highly positive correlations in pairwise combinations. We sequenced the Chinese peanut mini-core collection using genotyping-by-sequencing approach and identified 105,814 high-quality single-nucleotide polymorphisms (SNPs). The population structure analysis showed essentially subspecies patterns in groups and obvious geographical distribution patterns in subgroups. A total of 79 significantly associated loci (P < 4.73 × 10–7) were detected for the six yield-related traits through GWAS. Of these, 31 associations were consistently detected in multiple environments, and 15 loci were commonly detected to be associated with multiple traits. Two major loci located on chromosomal pseudomolecules A06 and A02 showed pleiotropic effects on yield-related traits, explaining ∼20% phenotypic variations across environments. The two genomic regions were found 46 putative candidate genes based on gene annotation and expression profile. The diagnostic marker for the yield-related traits from non-synonymous SNP (Aradu-A06-107901527) was successfully validated, achieving a high correlation between nucleotide polymorphism and phenotypic variation. This study provided insights into the genetic basis of yield-related traits in peanut and verified one diagnostic marker to facilitate marker-assisted selection for developing high-yield peanut varieties.

Peanut is an important legume crop worldwide. To uncover the genetic basis of yield features and assist breeding in the future, we conducted genome-wide association studies (GWAS) for six yield-related traits of the Chinese peanut mini-core collection. The seed (pod) size and weight of the population were investigated under four different environments, and these traits showed highly positive correlations in pairwise combinations. We sequenced the Chinese peanut mini-core collection using genotyping-by-sequencing approach and identified 105,814 high-quality single-nucleotide polymorphisms (SNPs). The population structure analysis showed essentially subspecies patterns in groups and obvious geographical distribution patterns in subgroups. A total of 79 significantly associated loci (P < 4.73 × 10–7) were detected for the six yield-related traits through GWAS. Of these, 31 associations were consistently detected in multiple environments, and 15 loci were commonly detected to be associated with multiple traits. Two major loci located on chromosomal pseudomolecules A06 and A02 showed pleiotropic effects on yield-related traits, explaining ∼20% phenotypic variations across environments. The two genomic regions were found 46 putative candidate genes based on gene annotation and expression profile. The diagnostic marker for the yield-related traits from non-synonymous SNP (Aradu-A06-107901527) was successfully validated, achieving a high correlation between nucleotide polymorphism and phenotypic variation. This study provided insights into the genetic basis of yield-related traits in peanut and verified one diagnostic marker to facilitate marker-assisted selection for developing high-yield peanut varieties. [ABSTRACT FROM AUTHOR]

Salinity is an increasing concern for the productivity of staple food crop. Crops with improved salt tolerance are highly needed to cultivate saline lands. Groundnut demand is increasing in countries like India, where saline land could be put under groundnut cultivation. The objective of this study was to identify groundnut genotypes with salinity tolerance for breeding programs. A set of 275 groundnut germplasm accessions were screened across three different seasons for salinity tolerance. Shoot biomass and seed yield under saline and non-saline conditions were recorded. Shoot biomass under saline conditions showed limited genotypic variation and was not determined as a selection criterion in the subsequent trials. While a six-fold range of variation for pod yield under salinity (10-12.5 dSm-1 NaCl) was observed. Pod weight under saline and control conditions had week correlation. Although there was a considerable genotypic variation of pod yield under saline conditions, the G×E interaction was observable as well. We report a set of 14 tolerant and 17 sensitive groundnut genotypes based on pod-seed yield and pod-seed numbers under saline conditions in the seasons studied. Among all the genotypes, ICGV 87187 and ICGS 76 were the most tolerant lines and ICG 6993 and ICG 4746 were the most susceptible lines in 2006 and 2006-2007, respectively. The suggested lines could be used in further breeding programs such as populations mapping. Our assumption to identify salt tolerant groundnut lines from selected landraces of putative saline areas did not help successfully to get more promising lines nevertheless the mini-core set of germplasm provided most of the salinity tolerant entries.

In the past five decades, constant research has been directed towards yield improvement in pigeonpea resulting in the deployment of several commercially acceptable cultivars in India. Though, the genesis of hybrid technology, the biggest breakthrough, enigma of stagnant productivity still remains unsolved. To sort this productivity disparity, genomic research along with conventional breeding was successfully initiated at ICRISAT. It endowed ample genomic resource providing insight in the pigeonpea genome combating production constraints in a precise and speedy manner. The availability of the draft genome sequence with a large‐scale marker resource, oriented the research towards trait mapping for flowering time, determinacy, fertility restoration, yield attributing traits and photo‐insensitivity. Defined core and mini‐core collection, still eased the pigeonpea breeding being accessible for existing genetic diversity and developing stress resistance. Modern genomic tools like next‐generation sequencing, genome‐wide selection helping in the appraisal of selection efficiency is leading towards next‐generation breeding, an awaited milestone in pigeonpea genetic enhancement. This paper emphasizes the ongoing genetic improvement in pigeonpea with an amalgam of conventional breeding as well as genomic research. [ABSTRACT FROM AUTHOR]

The seeds of chickpea provide an exceptional source of dietary proteins and is one of the important legumes in both developed and developing countries over the world. The available germplasm of cultivated chickpea is deficient in desired biochemical signatures. To identify new sources of variations for breeding, reduced subsets of germplasm such as mini-core collection can be explored as an effective resource. In the present investigation, mini-core collections consisting of 215 accessions of chickpea were extensively evaluated for tapping biochemical diversity. Analysis included ten biochemical parameters comprising total protein, total free amino acids, phytic acid, tannin, total phenolics, total flavonoids, lectin, DPPH radical scavenging activity, in vitro digestibility of protein and starch. The spectrum of diversity was documented for total protein (4.60-33.90%), total free amino acids (0.092-9.33 mg/g), phytic acid (0.009-4.06 mg/g), tannin (0.232-189.63 mg/g), total phenolics (0.15-0.81 mg/g), total flavonoids (0.04-1.57 mg/g), lectin (0.07-330.32 HU/mg), DPPH radical scavenging activity (26.74-49.11%), in vitro protein digestibility (59.45-76.22%) and in vitro starch digestibility (45.63-298.39 mg of maltose/g). The principal component analysis revealed association of chickpea higher protein content to the lower level of total phenolics and flavonoid contents. The dendrogram obtained by unweighted pair group method using arithmetic average cluster analysis grouped the chickpea accessions into two major clusters. This is the first comprehensive report on biochemical diversity analysed in the mini-core chickpea accessions. The ultimate purpose of conducting such studies was to deliver information on nutritional characteristics for effective breeding programmes. Depending on the objectives of the breeding aforesaid accessions could be employed as a parent. [ABSTRACT FROM AUTHOR]

The sugarcane germplasm collection located in Khuzestan, Iran, is one of the most important genetic resources with valuable accessions from different continents. However, this collection has not been properly used by breeders due to the extremely large population. The aim of this study was to phenotypically characterize the sugarcane germplasm and form a mini-core collection. Hence, 13 morphological traits were evaluated on 253 accessions. The primary germplasm was grouped into 10 clusters based on partial repeated bisection (RB) data, where the smallest cluster contained three accessions from two breeding centres (USA and Cuba). Using principal component analysis (PCA), the first two PCs (principal component) explained 59.5% of the total variation. A mini-core of 21 accessions was created by using the maximization strategy, with a low mean difference percentage (MD = 2.31%) and large coincidence rate of range (CR = 93.96%). The sugarcane mini-core represented the major diversity of the primary collection. The means and medians between the mini-core and the primary collection did not differ significantly. Accessions with high sugar and cane yield, originating from the USA, Cuba, Argentina, and South Africa, were in the mini-core collection. In this paper, we established, for the first time, an applied mini-core collection in sugarcane germplasm. The mini-core collection, as a breeding collection, is a highly suitable, manageable, and efficient subset for the enhanced use of sugarcane germplasm in breeding programs. [ABSTRACT FROM AUTHOR]

Protein percentage and mineral concentrations are important parameters for determining the seed nutrition quality. Although the U.S. peanut mini-core collection is the important genetic resources for peanut breeding programs, the variability in protein percentage and mineral concentrations for this mini-core has not been well evaluated. The lack of information may hinder its optimum utilization. The seeds from this mini-core were collected from two field seasons. Their protein percentage and mineral concentrations of 95 accessions were determined by nitrogen analysis and inductively coupled plasma - optical emission spectrometry, respectively. Significant variability in the seed protein percentage among accessions was revealed, ranging from 20.6 to 30.4%, with an average of 26.2%. Significantly higher variability in plant micronutrient mineral concentrations (more than two-fold for B, Cu, Fe, Mn, Mo, Na, Ni, and Zn) than in macronutrient mineral concentrations (less than two-fold for K, Mg, P, and S) was also identified among accessions. Calcium however was an exception, demonstrating 3.7-fold variability among the accessions evaluated. Three accessions (PI 497517, PI 493547, and PI 429429) were identified as lines containing high seed levels of both Fe and Zn. Correlation coefficients were also determined among 28 investigated seed chemical composition traits, using data from a previous study with the same samples. Protein percentage was significantly negatively correlated with seed weight, oil, and oleate percentage. Several mineral elements (Fe, Mg, Mn, and Zn) were also significantly negatively correlated with oleate percentage. The results from this study will be useful for peanut nutrition breeding and food product development. [ABSTRACT FROM AUTHOR]

The sugarcane germplasm collection located in Khuzestan, Iran, is one of the most important genetic resources with valuable accessions from different continents. However, this collection has not been properly used by breeders due to the extremely large population. The aim of this study was to phenotypically characterize the sugarcane germplasm and form a mini-core collection. Hence, 13 morphological traits were evaluated on 253 accessions. The primary germplasm was grouped into 10 clusters based on partial repeated bisection (RB) data, where the smallest cluster contained three accessions from two breeding centres (USA and Cuba). Using principal component analysis (PCA), the first two PCs (principal component) explained 59.5% of the total variation. A mini-core of 21 accessions was created by using the maximization strategy, with a low mean difference percentage (MD = 2.31%) and large coincidence rate of range (CR = 93.96%). The sugarcane mini-core represented the major diversity of the primary collection. The means and medians between the mini-core and the primary collection did not differ significantly. Accessions with high sugar and cane yield, originating from the USA, Cuba, Argentina, and South Africa, were in the mini-core collection. In this paper, we established, for the first time, an applied mini-core collection in sugarcane germplasm. The mini-core collection, as a breeding collection, is a highly suitable, manageable, and efficient subset for the enhanced use of sugarcane germplasm in breeding programs.

Association mapping is a powerful approach for exploring the molecular basis of phenotypic variations in plants. A peanut (Arachis hypogaea L.) mini-core collection in China comprising 298 accessions was genotyped using 109 simple sequence repeat (SSR)markers, which identified 554 SSR alleles and phenotyped for 15 agronomic traits in three different environments, exhibiting abundant genetic and phenotypic diversity within the panel. A model-based structure analysis assigned all accessions to three groups. Most of the accessions had the relative kinship of less than 0.05, indicating that there were no or weak relationships between accessions of the minicore collection. For 15 agronomic traits in the peanut panel, generally the Q+K model exhibited the best performance to eliminate the false associated positives compared to the Q model and the general linear model-simple model. In total, 89 SSR alleles were identified to be associated with 15 agronomic traits of three environments by the Q+K model-based association analysis. Of these, eight alleles were repeatedly detected in two or three environments, and 15 alleles were commonly detected to be associated with multiple agronomic traits. Simple sequence repeat allelic effects confirmed significant differences between different genotypes of these repeatedly detected markers. Our results demonstrate the great potential of integrating the association analysis and marker-assisted breeding by utilizing the peanut mini-core collection. [ABSTRACT FROM AUTHOR]

Background: Sesame (Sesamum indicum L.) is one of the four major oil crops in China. A sesame core collection (CC) was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC). Results: Results from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525). The Shannon-Weaver diversity index (I) and Nei genetic diversity index (h) were higher (I = 0.9537, h = 0.5490) when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218). A mini-core collection (MC) containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%), low variance difference percentage (VD, 22.58%), large variable rate of coefficient of variance (VR, 114.86%), and large coincidence rate of range (CR, 95.76%). For molecular data, the diversity indices and the polymorphism information content (PIC) for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven. Conclusions: This study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and large VR% and CR% suggested that the MC provides a good representation of the genetic diversity of the original CC. The MC was more genetically diverse with higher diversity indices and a higher PIC value than the CC. A MC may aid in reasonably and efficiently selecting materials for sesame breeding and for genotypic biological studies, and may also be used as a population for association mapping in sesame. [ABSTRACT FROM AUTHOR]

rice mini-core collection consisting of 217 accessions has been developed to represent the USDA core and whole collections that include 1,794 and 18,709 accessions, respectively. To improve the efficiency of mining valuable genes and broadening the genetic diversity in breeding, genetic structure and diversity were analyzed using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core had 13.5 alleles per locus, which is the most among the reported germplasm collections of rice. Similarly, polymorphic information content (PIC) value was 0.71 in the mini-core which is the highest with one exception. The high genetic diversity in the mini-core suggests there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. A model-based clustering analysis resulted in lowland rice including three groups, aus (39 accessions), indica (71) and their admixtures (5) , upland rice including temperate japonica (32), tropical japonica (40), aromatic (6) and their admixtures (12) and wild rice (12) including glaberrima and four other species of Oryza. Group differentiation was analyzed using both genotypic distance Fst from 128 molecular markers and phenotypic (Mahalanobis) distance D from 14 traits. Both dendrograms built by Fst and D reached similar-differentiative relationship among these genetic groups, and the correlation coefficient showed high value 0.85 between Fst matrix and D matrix. The information of genetic and phenotypic differentiation could be helpful for the association mapping of genes of interest. Analysis of genotypic and phenotypic diversity based on genetic structure would facilitate parent selection for broadening genetic base of modern rice cultivars via breeding effort. [ABSTRACT FROM AUTHOR]

Cultivated peanut, the second most economically important legume crop throughout the United States and the third most important oilseed in the world, is consistently threatened by various diseases and pests. Sclerotinia minor Jagger ( S. minor), the causal agent of Sclerotinia blight, is a major threat to peanut production in the Southwestern U.S., Virginia, and North Carolina and can reduce yield by up to 50% in severely infested fields. Although host plant resistance would provide the most effective solution to managing Sclerotinia blight, limited sources of resistance to the disease are available for use in breeding programs. Peanut germplasm collections are available for exploration and identification of new sources of resistance, but traditionally the process is lengthy, requiring years of field testing before those potential sources can be identified. Molecular markers associated with phenotypic traits can speed up the screening of germplasm accessions, but until recently none were available for Sclerotinia blight resistance in peanut. This study objective of this study was to characterize the US peanut mini-core collection with regards to a recently discovered molecular marker associated with Sclerotinia blight resistance. Ninety-six accessions from the collection were available and genotyped using the SSR marker and 39 total accessions from spanish, valencia, runner market types were identified as new potential sources of resistance and targeted for further evaluation in field tests for Sclerotinia blight resistance. [ABSTRACT FROM AUTHOR]

Abstract: Salinity is an ever-increasing problem in agriculture worldwide, especially in South Asia (India, Pakistan) and Australia. Improved genotypes that are well adapted to saline conditions are needed to enhance and sustain production in these areas. A screening of 263 accessions of chickpea, including 211 accessions from ICRISAT''s mini-core collection (10% of the core collection and 1% of the entire collection), showed a 6-fold range of variation for seed yield under salinity (1.9L of 80mM NaCl per 7.5kg Vertisol), with several genotypes yielding 20% more than a previously released salinity tolerant cultivar. The range of variation in yields under salinity was similar in both kabuli and desi chickpeas, indicating that breeding for salinity tolerance can be undertaken in both groups. A strong relationship (r 2 =0.50) was found between the seed yield under salinity and the seed yield under a non-saline control treatment, indicating that the seed yield under salinity was explained in part by a yield potential component and in part by salinity tolerance per se. Seed yields under salinity were therefore computed to separate the yield potential component from the residuals that accounted for salinity tolerance per se. Among the genotypes evaluated, desi genotypes had higher salinity tolerance than kabuli genotypes. The residuals were highly correlated to the ratio of seed yield under salinity to that of the control, indicating that both parameters can be used to assess salinity tolerance. A similar ratio was calculated for shoot dry weight at 50 days after sowing. However, no significant correlation was found between the shoot dry weight ratio and the yield ratio, indicating that differences in salinity tolerance among genotypes could not be inferred from measurements in the vegetative stage. The major trait related to salinity tolerance was the ability to maintain a large number of filled pods, whereas seed size was similar in tolerant and sensitive genotypes. Salinity tolerance was not related to the shoot Na+ or K+ concentrations. [Copyright &y& Elsevier]

Extensive and deep root systems have been recognized as one of the most important traits for improving chickpea ( Cicer arietinum L.) productivity under progressively receding soil moisture conditions. However, available information on the range of variation for root traits is still limited. Genetic variability for the root traits was investigated using a cylinder culture system during two consecutive growth seasons in the mini-core germplasm collection of ICRISAT plus several wild relatives of chickpea. The largest genetic variability was observed at 35 days after sowing for root length density (RLD) (heritability, h 2 = 0.51 and 0.54) across seasons, and followed by the ratio of plant dry weight to root length density with h 2 of 0.37 and 0.50 for first and second season, respectively. The root growth of chickpea wild relatives was relatively poor compared to C. arietinum, except in case of C. reticulatum. An outstanding genotype, ICC 8261, which had the largest RLD and one of the deepest root system, was identified in chickpea mini-core germplasm collection. The accession ICC 4958 which was previously characterized as a source for drought avoidance in chickpea was confirmed as one with the most prolific and deep root system, although many superior accessions were also identified. The chickpea landraces collected from the Mediterranean and the west Asian region showed a significantly larger RLD than those from the south Asian region. In addition, the landraces originating from central Asia (former Soviet Union), characterized by arid agro-climatic conditions, also showed relatively larger RLD. As these regions are under-represented in the chickpea collection, they might be interesting areas for further germplasm exploration to identify new landraces with large RLD. The information on the genetic variability of chickpea root traits provides valuable baseline knowledge for further progress on the selection and breeding for drought avoidance root traits in chickpea. [ABSTRACT FROM AUTHOR]

Abstract Background Sesame (Sesamum indicum L.) is one of the four major oil crops in China. A sesame core collection (CC) was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC). Results Results from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525). The Shannon-Weaver diversity index (I) and Nei genetic diversity index (h) were higher (I = 0.9537, h = 0.5490) when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218). A mini-core collection (MC) containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%), low variance difference percentage (VD, 22.58%), large variable rate of coefficient of variance (VR, 114.86%), and large coincidence rate of range (CR, 95.76%). For molecular data, the diversity indices and the polymorphism information content (PIC) for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven. Conclusions This study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and large VR% and CR% suggested that the MC provides a good representation of the genetic diversity of the original CC. The MC was more genetically diverse with higher diversity indices and a higher PIC value than the CC. A MC may aid in reasonably and efficiently selecting materials for sesame breeding and for genotypic biological studies, and may also be used as a population for association mapping in sesame.