Mini Core Research Articles

Grain Nutrient Composition of Maize (Zea mays L.) Drought-Tolerant Populations.

A total of 13 maize populations from the drought-tolerant mini core collection from Maize Research Institute gene bank were evaluated for oil, protein, and tryptophan contents, fatty acid (FA) composition, and kernel characteristics. All accessions are high oil (5.8-7.9%) and protein (10.58-12.45%) genotypes. Most of the accessions showed high contents of tryptophan (0.070-0.081%) and saturated (12.65-17.91%) and monounsaturated (24.19-45.52%) FAs. Significant positive correlations were found between oil and protein and between oil and tryptophan contents (p < 0.01). Correlations between oil and principal FA were non-significant. Several accessions showed multiple nutritional advantages. For example, IP6428 had high oil (7.3%), tryptophan (0.081%), and saturated FA (17.9%) contents. Moreover, a positive correlation (p < 0.01) between palmitic (13.68%) and oleic (34.74%) acids enables the use of IP6428 for developing lines high in these FAs. Because drought-tolerant accessions were selected in both subtropical and temperate zones, they could be used for breeding value-added maize adapted to both environments.

Coupling of the 3D neutron kinetic core model DYN3D with the CFD software ANSYS-CFX

This article presents the implementation of a coupling between the 3D neutron kinetic core model DYN3D and the commercial, general purpose computational fluid dynamics (CFD) software ANSYS-CFX. In the coupling approach, parts of the thermal hydraulic calculation are transferred to CFX for its better ability to simulate the three-dimensional coolant redistribution in the reactor core region. The calculation of the heat transfer from the fuel into the coolant remains with DYN3D, which incorporates well tested and validated heat transfer models for rod-type fuel elements. On the CFX side, the core region is modeled based on the porous body approach. The implementation of the code coupling is verified by comparing test case results with reference solutions of the DYN3D standalone version. Test cases cover mini and full core geometries, control rod movement and partial overcooling transients.

DEVELOPMENT OF PCR-BASED SNP MARKER OF RICE Waxy GENE WITH CONFRONTING TWO-PAIR PRIMERS.

Rice amylose content (AC) is a key determinant for grain end-use quality attributes. The base substitution (G --> T) at +1 loci of the first intron (In1) of Waxy (Wx), a major gene controlling AC in rice, results in decreased AC. A new SNP typing method of Wx In1 based on polymerase chain reaction with confronting two-pair primers (PCR-CTPP) was reported here: first its practicability was confirmed by 23 varieties with known SN P and AC; and then the segregation ratio at target SN P loci were checked and it fitted well for 1 :2: 1 single gene segregation; at last SNP typing and AC assay with 150 mini core collections (MCC) in China showed that average AC of 53 G type varieties (22.5%) was significantly higher than that of 97 T type varieties (13.7%) (p < 0.01) and the target SNP loci explained 77.8% AC variation. So this method could be used to estimate AC of rice variety roughly or in marker-assisted-breeding, that is, using variety with known and desired AC as Wx allele donor parent and aided with crossbreed, backcross and marker-assisted selection (MAS) reported here rice breeders could improve AC of varieties with comprehensively excellent performance to meet special end-products.

Interrelationships and genetic analysis of seed yield and morphological traits in mini core collection of Iranian landrace, breeding lines and improved chickpea (Cicer arietinum L.) cultivars

To determine the association between genetic parameters and morphological traits in chickpea (Cicer arietinum L.) genotypes, a field experiment was conducted with 49 different landrace, breeding lines and cultivated chickpea genotypes using a 7?7 lattice square design with 2 replications in the 2012-2013 growing season. Genetic parameters including genetic, environmental and phenotypic variances; coefficients of variation; heritability; correlation coefficients; factor analysis and path coefficients were estimated, and cluster analysis was performed. High heritability values observed in measured traits indicating that these traits are controlled mainly by additive genes and that selection of such traits may be effective for improving seed yield. Number of seeds per plant, 100-seed weight and plant biomass had a positive direct effect on seed yield. These traits also had positive and highly significant phenotypic correlations with seed yield. Using principal component (PC) analysis, the first three PCs with eigenvalues more than 1 contributed 70.94% of the variability among accessions. The germplasm were grouped into 3 clusters. Each cluster had some specific characteristics of its own and the cluster I was clearly separated from cluster II and III. Overall the results, it can be concluded that seed yield in chickpea can be improved by selecting an ideotype having greater number of seeds per plant, 100-seed weight and plant biomass.

Genetic diversity and establishment of a core collection of oil palm (Elaeis guineensisJacq.) based on molecular data

Understanding of genetic diversity and its distribution is essential for promoting the use of genetic resources. The development of core collections using molecular tools has been proposed as a strategy for increasing the economical use and conservation of genetic resources. In this study, we investigated the genetic variation among different geographical origins and potential entries that constituted a core collection of oil palm, using 29 microsatellite markers and by evaluating 788 oil palm accessions. Our results revealed important genetic diversity (HT= 0.759) between oil palm accessions from Angola and Cameroon, which exhibited a low coefficient of genetic differentiation between populations (GST= 0.022). However, the inclusion of oil palm accessions from Indonesia in the analysis resulted in a high coefficient of genetic differentiation between populations (GST= 0.251). We found that the combination of stratified sampling based on a sorting method and a heuristic algorithm was the most effective method for the development of an oil palm core collection set. Using this method, two core collections were identified. The first core collection, comprising 289 entries, contained 271 retained alleles in a sample representing 37% of the entire collection. The second one is a mini core collection, comprising 91 entries, that contained 271 retained alleles with a totalHevalue of 0.72 in a sample representing 11% of the entire collection. The information reported in this study will be of great interest to oil palm researchers because new strategies for breeding programmes can be developed based on these advances.

Influence of low-molecular-weight glutenin subunit genes at Glu-A3 locus on wheat sodium dodecyl sulfate sedimentation volume and solvent retention capacity value.

To understand the effect of low-molecular-weight (LMW) glutenin alleles at the Glu-A3 locus on sodium dodecyl sulfate (SDS) sedimentation volume and solvent retention capacity (SRC) values, 244 accessions of Chinese wheat (Triticum aestivum L.) mini core collections were investigated. In this study the significant differences in wholemeal flour SDS sedimentation volume and SRC values associated with specific glutenin alleles at the Glu-A3 locus were explained. Seven glutenin alleles at the Glu-A3 locus were confirmed by locus-specific polymerase chain reaction (PCR). SDS sedimentation volume and lactic acid SRC value were significantly affected by alleles Glu-A3b and Glu-A3g. Based on total average values, 28 varieties carrying Glu-A3b had significantly higher means of SDS sedimentation volume and lactic acid SRC value, whereas 19 varieties carrying Glu-A3g had significantly lower means. Alleles Glu-A3d and Glu-A3f significantly increased only SDS sedimentation volume and sucrose SRC value respectively. Correlation analysis showed that SDS sedimentation volume was uncorrelated with lactic acid SRC and sucrose SRC values. The Glu-A3 LMW glutenin subunit could predict 12.8% of the variance in SDS sedimentation volume, 4.7% in lactic acid SRC and 6.4% in sucrose SRC.

Genetic Variability and Effect of Postflowering Drought on Stalk Sugar Content in Sorghum Mini Core Collection

ABSTRACTSweet sorghum [Sorghum bicolor (L.) Moench] is an important food, feed, and biofuel crop worldwide. Its stalks are rich in sugar, largely influenced by environments and crop stage when the stalks are harvested. This study evaluated sorghum mini core collection for stalk sugar content on the basis of Brix, phenology, and agronomic traits. Accessions were first classified into five groups based on flowering to match crop phenology, which together with controls were separately grown in split‐plot design in vertisol under irrigated and drought stress conditions for two postrainy seasons. The main and interaction effects were significant for most of the traits. Drought stress significantly increased the mean Brix (12.11 to 26.76%) in four of the five groups of accessions. The mean Brix increased under drought in 169 accessions, decreased in one accession, while the remaining accessions were not affected. IS 13294, 13549, 23216, 23684, 24139, 24939, and 24953 significantly recorded greater mean Brix (14.0 to 15.2%) as compared with best control, IS 33844 (12.4%), across environments. However, these accessions had lower yields and lower 100‐seed weight. In contrast, IS 1004, 4698, 23891, and 28141 significantly outyielded IS 33844 by 11.7 to 22.7% and had almost the same Brix content (∼13%). A hierarchical tree diagram grouped these accessions into two distinct clusters: accessions with significantly greater Brix but lower yield and those with high yield but with Brix similar to IS 33844. The grouping also separated accessions largely on the basis of geographic regions and racial classification. The identified accessions are ideal resources for the development of cultivars with bioenergy traits.

TEF-7A, a transcript elongation factor gene, influences yield-related traits in bread wheat (Triticum aestivum L.).

In this study, TaTEF-7A, a member of the transcript elongation factor gene family, and its flanking sequences were isolated. TaTEF-7A was located on chromosome 7A and was flanked by markers Xwmc83 and XP3156.3. Subcellular localization revealed that TaTEF-7A protein was localized in the nucleus. This gene was expressed in all organs, but the highest expression occurred in young spikes and developing seeds. Overexpression of TaTEF-7A in Arabidopsis thaliana produced pleiotropic effects on vegetative and reproductive development that enhanced grain length, silique number, and silique length. No diversity was found in the coding region of TaTEF-7A, but 16 single nucleotide polymorphisms and Indels were detected in the promoter regions of different cultivars. Markers based on sequence variations in the promoter regions (InDel-629 and InDel-604) were developed, and three haplotypes were identified based on those markers. Haplotype-trait association analysis of the Chinese wheat mini core collection revealed that TaTEF-7A was significantly associated with grain number per spike. Phenotyping of near-isogenic lines (NILs) confirmed that TaTEF-7A increases potential grain yield and yield-related traits. Frequency changes in favoured haplotypes gradually increased in cultivars released in China from the 1940s. Geographic distributions of favoured haplotypes were characterized in six major wheat production regions worldwide. The presence of Hap-7A-3, the favoured haplotype, showed a positive correlation with yield in a global set of breeding lines. These results suggest that TaTEF-7A is a functional regulatory factor for grain number per spike and provide a basis for marker-assisted selection.

Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers.

Chickpea is an important food legume crop for the semi-arid regions, however, its productivity is adversely affected by various biotic and abiotic stresses. Identification of candidate genes associated with abiotic stress response will help breeding efforts aiming to enhance its productivity. With this objective, 10 abiotic stress responsive candidate genes were selected on the basis of prior knowledge of this complex trait. These 10 genes were subjected to allele specific sequencing across a chickpea reference set comprising 300 genotypes including 211 genotypes of chickpea mini core collection. A total of 1.3 Mbp sequence data were generated. Multiple sequence alignment (MSA) revealed 79 SNPs and 41 indels in nine genes while the CAP2 gene was found to be conserved across all the genotypes. Among 10 candidate genes, the maximum number of SNPs (34) was observed in abscisic acid stress and ripening (ASR) gene including 22 transitions, 11 transversions and one tri-allelic SNP. Nucleotide diversity varied from 0.0004 to 0.0029 while polymorphism information content (PIC) values ranged from 0.01 (AKIN gene) to 0.43 (CAP2 promoter). Haplotype analysis revealed that alleles were represented by more than two haplotype blocks, except alleles of the CAP2 and sucrose synthase (SuSy) gene, where only one haplotype was identified. These genes can be used for association analysis and if validated, may be useful for enhancing abiotic stress, including drought tolerance, through molecular breeding.

Erratum to: Association mapping of maturity and plant height using SNP markers with the sorghum mini core collection

Erratum to: Association mapping of maturity and plant height using SNP markers with the sorghum mini core collection

Genetic variation of functional components in brown rice of mini core collection of Yunnan landrace rice and its advanced backcross lines

Ninety-five assessions from the mini core collection of Yunnan rice and their advanced backcross lines,which were obtained using the 95 accessions as donor,the Diantun 502 as the recurrent parent of Indica rice and the Hexi35 as the recurrent parent of japonica rice,were tested for their genetic variation,and the content of 3 functional components,namely,total flavonoids(TF),γ-aminobutyric acid(GABA) and resistant starch(RS) in the brown rice were determined.The results show that(1) there are significant difference in the variation coefficients and the ranges of FL,GABA and RS contents,with RS showing the highest variation coefficients followed by GABA and TF.(2) the contents of 3 functional components in brown rice of the acceptor are low,which were increased in the corresponding advanced backcross lines,the content of total flavonoids in brown rice of the donor were significantly higher than those of the advanced backcross lines,the content of GABA in brown rice of japonica advanced backcross lines was higher than those of the corresponding donor.The content of RS in brown rice of the donor and its advanced backcross lines are bimodally distributed,with low genetic variation,indicating the the content of RS is controlled by genotype.

Multiple Resistant and Nutritionally Dense Germplasm Identified from Mini Core Collection in Peanut

ABSTRACTPeanut (Arachis hypogaea L.) is extensively grown by resource‐poor farmers in the semiarid tropics where many abiotic and biotic stresses limit the crop's productivity and seed quality. Peanut cultivars with enhanced host‐plant resistance, adaptation to abiotic stress, input‐use efficiency, and yield potential will maximize yield gains and minimize inputs to sustain production. The peanut mini core collection was evaluated for agronomic traits in multienvironment trials at Patancheru, India. The published information on 184 mini core accessions revealed 28 accessions resistant to abiotic stress, 30 resistant to biotic stress, and 18 that were agronomically desirable but susceptible to stresses, while 16 were seed nutrient dense. The mini core is part of the composite collection, which was previously genotyped using SSRs. The agronomic evaluation, stress response, and nutritional information together with genotyping data were used to identify genetically diverse germplasm with agronomically beneficial traits: ICG 12625 (resistance to drought, low temperature, late leaf spot [LLS], Aspergillus flavus Link, bacterial wilt; high oil and good oil quality) and ICG 442 (resistance to drought, salinity, P deficiency); ICG 12625 and ICG 2381 (resistance to rust, A. flavus; good oil quality); ICG 12697 (resistance to LLS, rust, A. flavus) and ICG 6022 (resistance to early leaf spot [ELS], LLS); ICG 14710 (high oil, Fe, Zn) and ICG 7963 (high protein, Fe, Zn); ICG 11426 (resistance to ELS, LLS, rust) and ICG 5221 (high Fe and Zn and good oil quality). Accessions with adaptation to rainy and/or post‐rainy environments were ICG# 434, 5745, 8285, 10036, 11088, 11651, 12625, 15042, and 15419. These accessions are ideal genetic resources that may be used to develop agronomically superior and nutritionally enhanced peanut cultivars with multiple resistances to abiotic and biotic stresses.

Agro-Morpho and Molecular Characterization of World Mini core Collections using Hypervariable Microsatellite Markers in Rice (Oryza sativaL.)

Mini core collection plays an important role in evaluating genetic resources hence, an attempt was made to characterize world mini core collections on the basis of 35 uniformly distributed hyper variable SSR molecular markers. Thirty five markers amplified a total of 131 allelic fragments with an average of 3.28 alleles per locus indicating high level of polymorphism among the analyzed rice lines. The two major clusters shown by PPS SRS technique indicated no difference for grouping japonica and indica genotypes. Therefore the allele specific amplification pattern was adapted for identification of particular genotypes. The similarity coefficients among the genotypes ranged from 0.58 to 0.83 with an average similarity value of 0.36. Maximum similarity value of 88% was observed between PR33319-9-1-1-5-3-5-4-1 and PR-114. Whereas minimum similarity value of 54% was found between TJ 50836 and TJ 35724 followed by TJ 39050 & TJ 35724 and TJ 50836 and NDR359 genotypes with 55% of genetic similarity. Breeders worldwide could use these findings to choice the germplasm for transferring characters

Screening of Groundnut (Arachis hypogaeaL.) Mini Core Collection against Late Leaf Spot Disease Caused byPhaeoisariopsis personata(Berk &amp; M.A Curtis van Arx)

Groundnut is considered as a “poor man's almond” possessing nutritional and medicinal properties constituting 44–50% edible oil, dietary protein (25–33%) and carbohydrates (20%). Diseases like early and late leaf spot caused by Cercospora arachidicola and Phaeoisariopsis personata and rust (Puccinia arachidis) are causing yield loss upto 70% resulting in a lower productivity of the crop. Germplasm collection is a reservoir of genetic variability comprising of promising genes for various characters that can be incorporated in the breeding programme to develop and broaden the genetic base of cultivars. Thus the investigation was carried out to screen the mini core collection comprising of 188 accessions representing fastigiata (33), vulgaris (71), peruviana (2), aequatoriana (1), hypogaea runner (33) and hypogaea bunch (48) and identify the genotypes resistant to late leaf spot. The experiment was conducted in a Simple Lattice Design (15 × 15) in two replications during kharif 2011 at UAS, Bangalore. The cultivar TMV-2 highly susceptible to late leaf spot was used as a spreader row for natural disease incidence. Phenotypic screening was done using modified nine point scale. The genotypes such as ICG 5286, ICG 2773, ICG 111426, ICG 2857 and ICG 6022 recorded as resistant to late leaf spot can be used as a donor of disease resistance in breeding of disease resistant cultivars. SSR marker GM 1009 was validated through single marker analysis.

Phenotypic characterization of a mini cor collection for increased grain quality in maize

Agronomic traits of 18 populations comprising a mini core collection for increased grain quality of the Maize Research Institute Zemun Polje were studied, along with two standard kernel type commercial hybrids. For almost all the traits (except root lodging) a considerable genetic variability was found, enabling successful breeding for any of them using this populations. Based on the obtained results, two populations were found to have grain yield at the level of ZP 341 commercial hybrid (one of them is from former Yugoslavia, and another is the introduced one). These two populations will be first to introduce into commercial breeding programs, if it proves they have also favorable biochemical characteristics. On the other hand, three populations had grain yield in the range of 1, 60-1, 91 t/ha, that is even lower than for commercial inbreeds. They will be excluded from the further breeding programs. Most of the populations were earlier than the commercial hybrids, during vegetation and according to the grain moisture at harvest. This is very favorable from a breeding standpoint. The worst characteristic of the population was very high stalk lodging, compared to commercial checks.

Establishment of the integrated applied core collection and its comparison with mini core collection in soybean (Glycine max)

The concept of core collection (CC) provides a new way of management and utilization of plant germplasm resources. In this study, an integrated applied core collection (IACC) of soybean was developed based on evaluation data for desirable agronomic and nutritional traits of available soybean germplasm resources including accessions with cold tolerance, drought tolerance, salt tolerance, soybean cyst nematode resistance, soybean mosaic virus resistance, high protein content, and high fat content. The newly formed collection encompasses accessions with high genetic diversity and desirable agronomic traits. The genetic diversity of the newly formed IACC was compared with that of the established mini core collection (MCC) of soybean with the aid of simple sequence repeat (SSR) markers and phenotypic traits. The results showed that at the molecular level, soybean IACC harbored a similar level of genetic diversity as the established MCC, and that at the phenotypic level the IACC encompasses more accessions with desirable traits than does the established MCC. The development of soybean IACC lays a foundation for breeding projects to meet different objectives in different eco-regions.

Mini Core Collection as a Resource to Identify New Sources of Variation

ABSTRACTIn chickpea, bottlenecks associated with its domestication and low use of germplasm in improvement programs have resulted in a narrow genetic base and its vulnerability to abiotic and biotic stresses. The core and mini core collections, representing diversity in the entire collection, have been advocated for enhanced utilization of germplasm in crop improvement. A chickpea mini core (211 accessions) was evaluated for agronomic traits from 2000 and 2001 to 2003 and 2004 in post‐rainy seasons under irrigated and non‐irrigated conditions. The published information on the response of chickpea mini core accessions to stress revealed that 40 accessions had resistance to abiotic stress, 31 to biotic stress, and 24 had no resistance to either of the stresses. The abiotic and biotic stress resistant groups had six accessions in common. The mini core collection accessions were also a part of composite collection accessions in chickpea, which was genotyped using 48 simple sequence repeats (SSRs; BMC Plant Biol. 8:106, 2008). The agronomic evaluation, stress response, and molecular profiling data on 93 accessions, including four controls, were used to identify genetically diverse germplasm with agronomically beneficial traits. A number of genetically diverse accessions possessing agronomically beneficial traits, such as ICC 440, 637, 1098, 3325, 3362, 4872, 7441, 8621, 9586, 10399, 12307, 14402, 15680, and 15686, which meet breeders’ needs, have been identified for use in breeding and genetics to map genomic regions associated with beneficial traits and as source materials for developing high yielding and widely adapted chickpea cultivars with multiple resistance to abiotic and biotic stress.

Exploiting Genomic Resources for Efficient Conservation and Use of Chickpea, Groundnut, and Pigeonpea Collections for Crop Improvement

Both chickpea (Cicer arietinum L.) and pigeonpea [Cajanus cajan (L.) Millsp.] are important dietary source of protein while groundnut (Arachis hypogaea L.) is one of the major oil crops. Globally, approximately 1.1 million grain legume accessions are conserved in genebanks, of which the ICRISAT genebank holds 49,485 accessions of cultivated species and wild relatives of chickpea, pigeonpea, and groundnut from 133 countries. These genetic resources are reservoirs of many useful genes for present and future crop improvement programs. Representative subsets in the form of core and mini core collections have been used to identify trait‐specific genetically diverse germplasm for use in breeding and genomic studies in these crops. Chickpea, groundnut, and pigeonpea have moved from “orphan” to “genomic resources rich crops.” The chickpea and pigeonpea genomes have been decoded, and the sequences of groundnut genome will soon be available. With the availability of these genomic resources, the germplasm curators, breeders, and molecular biologists will have abundant opportunities to enhance the efficiency of genebank operations, mine allelic variations in germplasm collection, identify genetically diverse germplasm with beneficial traits, broaden the cultigen's genepool, and accelerate the cultivar development to address new challenges to production, particularly with respect to climate change and variability. Marker‐assisted breeding approaches have already been initiated for some traits in chickpea and groundnut, which should lead to enhanced efficiency and efficacy of crop improvement. Resistance to some pests and diseases has been successfully transferred from wild relatives to cultivated species.

Mapping and candidate genes associated with saccharification yield in sorghum

Sorghum (Sorghum bicolor (L.) Moench) is a high-yielding, stress tolerant energy crop for lignocellulosic-based biofuel production. Saccharification is a process by which hydrolytic enzymes break down lignocellulosic materials to fermentable sugars for biofuel production, and mapping and identifying genes underlying saccharification yield is an important first step to genetically improve the plant for higher biofuel productivity. In this study, we used the ICRISAT sorghum mini core germplasm collection and 14 739 single nucleotide polymorphism markers to map saccharification yield. Seven marker loci were associated with saccharification yield and five of these loci were syntenic with regions in the maize genome that contain quantitative trait loci underlying saccharification yield and cell wall component traits. Candidate genes from the seven loci were identified but must be validated, with the most promising candidates being β-tubulin, which determines the orientation of cellulose microfibrils in plant secondary cell walls, and NST1, a master transcription factor controlling secondary cell wall biosynthesis in fibers. Other candidate genes underlying the different saccharification loci included genes that play a role in vascular development and suberin deposition in plants. The identified loci and candidate genes provide information into the factors controlling saccharification yield and may facilitate increasing biofuel production in sorghum.

SNP markers linked to leaf rust and grain mold resistance in sorghum

Grain mold and rust are diseases that can significantly reduce sorghum grain yield. Breeding for resistance to these diseases is hindered by inefficient disease screening. A viable option to greatly improve breeding efficiency is to identify molecular markers or genes linked to the host resistance. In this study, we applied 14,739 single nucleotide polymorphism markers to the sorghum mini core of 242 accessions that had been evaluated for rust resistance in both greenhouse and field and for grain mold in the field for 2 years. Through association mapping we have identified two loci linked to grain mold resistance and five loci linked to rust resistance. Among the two loci linked to grain mold resistance, one contained a homolog of the maize nonhost resistance gene Rxo1. Two of rust-linked loci each contained the rust resistance gene homologous to the maize rust resistance gene Rp1-D which is the B locus (the A locus containing Pu was not linked in this study) and to the wheat rust resistance gene Lr1. The remaining loci contained genes important in other steps of the defense response, such as cyclophilins that mediate resistance response preceding hypersensitive response (HR) and Hin1 directly involved in producing HR. The results from this study will facilitate marker-assisted selection of host resistance to grain mold and rust in sorghum.