Mini Core Research Articles

Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection.

Root-lesion nematodes (RLN) pose a significant threat to chickpea (Cicer arietinum L.) by damaging the root system and causing up to 25% economic losses due to reduced yield. Worldwide commercially grown chickpea varieties lack significant genetic resistance to RLN, necessitating the identification of genetic variants contributing to natural resistance. This study identifies genomic loci responsible for resistance to the RLN, Pratylenchus thornei Sher & Allen, in chickpea by utilizing high-quality single nucleotide polymorphisms from whole-genome sequencing data of 202 chickpea accessions. Phenotypic evaluations of the genetically diverse set of chickpea accessions in India and Australia revealed a wide range of responses from resistant to susceptible. Genome-wide association studies (GWAS) employing Fixed and Random Model Circulating Probability Unification (FarmCPU) and Bayesian-Information and Linkage-Disequilibrium Iteratively Nested Keyway (BLINK) models identified 44 marker-trait associations distributed across all chromosomes except Ca1. Crucially, genomic regions on Ca2 and Ca5 consistently display significant associations across locations. Of 25 candidate genes identified, five genes were putatively involved in RLN resistance response (glucose-6-phosphate dehydrogenase, heat shock proteins, MYB-like DNA-binding protein, zinc finger FYVE protein and pathogenesis-related thaumatin-like protein). One notably identified gene (Ca_10016) presents four haplotypes, where haplotypes 1-3 confer moderate susceptibility, and haplotype 4 contributes to high susceptibility to RLN. This information provides potential targets for marker development to enhance breeding for RLN resistance in chickpea. Additionally, five potential resistant genotypes (ICC3512, ICC8855, ICC5337, ICC8950, and ICC6537) to P. thornei were identified based on their performance at a specific location. The study's significance lies in its comprehensive approach, integrating multiple-location phenotypic evaluations, advanced GWAS models, and functional genomics to unravel the genetic basis of P. thornei resistance. The identified genomic regions, candidate genes, and haplotypes offer valuable insights for breeding strategies, paving the way for developing chickpea varieties resilient to P. thornei attack.

Promiscuous potato: elucidating genetic identity and the complex genetic relationships of a cultivated potato germplasm collection.

A total of 3,860 accessions from the global in trust clonal potato germplasm collection w3ere genotyped with the Illumina Infinium SolCAP V2 12K potato SNP array to evaluate genetic diversity and population structure within the potato germplasm collection. Diploid, triploid, tetraploid, and pentaploid accessions were included representing the cultivated potato taxa. Heterozygosity ranged from 9.7% to 66.6% increasing with ploidy level with an average heterozygosity of 33.5%. Identity, relatedness, and ancestry were evaluated using hierarchal clustering and model-based Bayesian admixture analyses. Errors in genetic identity were revealed in a side-by-side comparison of in vitro clonal material with the original mother plants revealing mistakes putatively occurring during decades of processing and handling. A phylogeny was constructed to evaluate inter- and intraspecific relationships which together with a STRUCTURE analysis supported both commonly used treatments of potato taxonomy. Accessions generally clustered based on taxonomic and ploidy classifications with some exceptions but did not consistently cluster by geographic origin. STRUCTURE analysis identified putative hybrids and suggested six genetic clusters in the cultivated potato collection with extensive gene flow occurring among the potato populations, implying most populations readily shared alleles and that introgression is common in potato. Solanum tuberosum subsp. andigena (ADG) and S. curtilobum (CUR) displayed significant admixture. ADG likely has extensive admixture due to its broad geographic distribution. Solanum phureja (PHU), Solanum chaucha (CHA)/Solanum stenotomum subsp. stenotomum (STN), and Solanum tuberosum subsp. tuberosum (TBR) populations had less admixture from an accession/population perspective relative to the species evaluated. A core and mini core subset from the genebank material was also constructed. SNP genotyping was also carried out on 745 accessions from the Seed Savers potato collection which confirmed no genetic duplication between the two potato collections, suggesting that the collections hold very different genetic resources of potato. The Infinium SNP Potato Array is a powerful tool that can provide diversity assessments, fingerprint genebank accessions for quality management programs, use in research and breeding, and provide insights into the complex genetic structure and hybrid origin of the diversity present in potato genetic resource collections.

Simulating Fuel Assembly Bowing: A Neutron-Diffusion Method Based on Arbitrary Quadrilateral Node and Conformal Mapping Technique

Fuel assembly bowing, widely observed in a pressurized water reactor (PWR), often results in an asymmetrical power distribution. This paper proposes a neutron-diffusion method that integrates the arbitrary quadrilateral node with the conformal mapping technique to characterize the impact of fuel assembly bowing on power distribution. The proposed method involves a nonlinear iteration process to solve the neutron-diffusion equation. The global coarse-mesh finite difference equation is established on the arbitrary quadrilateral nodes, which are redivided in response to fuel assembly bowing. The local two-node nodal expansion method equation is established on the rectangular nodes, which are mapped from the original arbitrary quadrilateral nodes using the conformal mapping technique. The proposed method has improved our self-developed core code, named SPARK, for PWRs. To verify this novel method, two distinct types of fuel assembly bowing are modeled based on the mini core. The reference results for these models were obtained using the Monte Carlo code NECP-MCX. The numerical results suggest a robust agreement between the biases of keff and power distributions and their corresponding reference results.

Genome-wide association study of plant color in Sorghum bicolor.

Sorghum plant color is the leaf sheath/leaf color and is associated with seed color, tannin and phenol content, head blight disease incidence, and phytoalexin production. In this study, we evaluated plant color of the sorghum mini core collection by scoring leaf sheath/leaf color at maturity as tan, red, or purple across three testing environments and performed genome-wide association mapping (GWAS) with 6,094,317 SNPs markers. Eight loci, one each on chromosomes 1, 2, 4, and 6 and two on chromosomes 5 and 9, were mapped. All loci contained one to three candidate genes. In qPC5-1, Sobic.005G165632 and Sobic.005G165700 were located in the same linkage disequilibrium (LD) block. In qPC6, Sobic.006G149650 and Sobic.006G149700 were located in the different LD block. The single peak in qPC6 covered one gene, Sobic.006G149700, which was a senescence regulator. We found a loose correlation between the degree of linkage and tissue/organ expression of the underlying genes possibly related to the plant color phenotype. Allele analysis indicated that none of the linked SNPs can differentiate between red and purple accessions whereas all linked SNPs can differentiate tan from red/purple accessions. The candidate genes and SNP markers may facilitate the elucidation of plant color development as well as molecular plant breeding.

English

Drought is a significant abiotic stress that negatively impacts plant growth and can lead to substantial crop yield losses. Our study aimed to establish selection criteria for 200 spring-wheat (Triticum aestivum L.) genotypes exposed to three different field-capacity (FC) levels (100%FC, 50%FC, 25%FC) in a growth chamber (seedling traits) and in the field under withholdirrigation conditions (yield traits). Variance, correlation, and principal component analysis (PCA) was performed to identify genotypes with high tolerance to drought stress. The stress induction significantly affects morphophysiological traits i.e., root length, root weight (fresh, dry), fresh shoot weight, relative water contents and root shoot ratio in spring wheat genotypes at seedling stage. The traits flag leaf area, spike weight, grain weight/spike, biological and grain yield were interlinked and strongly influenced by drought in the field. The mean grain yield performance decreased from 21.85 g to 19.46 g under variable water regimes; however, the differences in harvest index and spikelets/spike were not significant. Among the tested genotypes, 9970 and 36-Eswyt-42 showed better root architecture development, leaf water management system, biological yield (66.07 g, 56.23 g) and grain yield (27.47 g, 28.78 g), respectively. The traits we identified may serve as an indirect selection index to enhance current semi-arid wheat germplasm and develop high-yielding drought-tolerant lines in advanced generations. Keywords: Mini core collection, Seedling and yield traits, Selection criteria, Variability analysis

Identification of B and R lines on maldandi cytoplasm and assessing their genetic diversity in rabi sorghum [Sorghum bicolor (L.) Moench

Fifty-four superior minicore collections were crossed with maldandi based male sterile line (M31-2A) to study restoration patterns andto classify maintainer (B) and restorer (R) lines. Of 54 mini core collections, only one came out as a strong restorer (IS 19450), 12 partialrestorers and 41 maintainers. Further, these 13 partial restorers (12 partial restorers and 1 strong restorer) and 41 maintainers alongwith M35-1 were subjected to diversity analysis for eleven characters. A total of 55 genotypes were clustered into seven clusters. Outof which, cluster–I and cluster-II had 34 and 16 genotypes, respectively, and five were solitary clusters having single genotypes. Thehighest inter-cluster distance was noted between cluster-VI and VII followed by cluster V and VI, and cluster-II and VII, indicating ample diversity available among them. Therefore, the genotypes of these clusters can be used as parents for crossing in the hybridization program to obtain desirable and excellent segregants. However, divergent maintainers against the strong restorer (IS 19450) can be used for the development of maldandi based hybrids.

Validation of yield associated molecular markers in a groundnut minicore collection

Groundnut is one of the world's most significant commercial oilseed crops. Previously, superior breeding lines and cultivars were primarily employed in most of the groundnut breeding programmes, resulting in a limited genetic base. A thorough evaluation of core collections makes it possible to access germplasm for crop development. A total of 184 mini core genotypes of groundnut were used for validating already reported 55 AhTE molecular markers (Arachis hypogaea transposable element) in the present study (6 AhTE markers for number of primary branches, 5 for plant height, 7 for pod yield per plant, 12 for number of pods per plant, 2 for shelling percentage, 12 for test weight, 9 for sound mature kernel weight percentage and 2 for oil content). Phenotyping was done during kharif 2018 (June to October) and twelve yield related parameters were recorded across 184 genotypes. Single marker analysis indicated a significant association of 40 markers (48 MTAs) at 5% probability level. Amongst these 48 MTAs, 39 MTAs exhibited utmost marker-trait associations with PVE estimate greater than 10%. Yield related AhTE markers validated in the present study might be used as viable tools for marker aided groundnut breeding for yield and yield-related parameters.

Multi-trait stability index for the identification of shoot fly (Atherigona soccata) resistant sorghum lines from a mini core collection.

On sorghum, shoot fly (Atherigona soccata Rondani) is the most destructive insect pest causing enormous economic losses. Breeding for host plant resistance is the best and economically viable strategy to control shoot fly damage. For improving resistance, there is a need to identify better donors with resistance, stability and adaptability. Sorghum mini core set representing global genetic diversity offers opportunity to understand genetic diversity of resistance component traits, their genotype × year (G × Y), and to identify better donors based on mean performance of multiple shoot fly resistance traits coupled with stability. Significant genetic variability and G × Y interaction was detected for all traits in the mini core set. Broad sense heritability and accuracy of selection for traits was high. Genetic correlation between deadhearts and leaf surface glossiness and with seedling height were negative while genetic correlation of deadhearts with oviposition was positive. The sorghum races did not establish any inherent relation with shoot fly resistance. Based on multiple trait stability index (MTSI), the study identified 12 stable resistant accessions. Selection differential and selection gains in the selected genotypes were positive for both glossiness and seedling height and were negative for deadhearts and Eggs. The MTSI selected new sources of resistance may constitute a breeding population for providing a dynamic gene pool of different resistance mechanisms for improving shoot fly resistance in sorghum. © 2023 Society of Chemical Industry.

Association mapping reveals novel genes and genomic regions controlling grain size architecture in mini core accessions of Indian National Genebank wheat germplasm collection.

Wheat (Triticum aestivum L.) is a staple food crop for the global human population, and thus wheat breeders are consistently working to enhance its yield worldwide. In this study, we utilized a sub-set of Indian wheat mini core germplasm to underpin the genetic architecture for seed shape-associated traits. The wheat mini core subset (125 accessions) was genotyped using 35K SNP array and evaluated for grain shape traits such as grain length (GL), grain width (GW), grain length, width ratio (GLWR), and thousand grain weight (TGW) across the seven different environments (E1, E2, E3, E4, E5, E5, E6, and E7). Marker-trait associations were determined using a multi-locus random-SNP-effect Mixed Linear Model (mrMLM) program. A total of 160 non-redundant quantitative trait nucleotides (QTNs) were identified for four grain shape traits using two or more GWAS models. Among these 160 QTNs, 27, 36, 38, and 35 QTNs were associated for GL, GW, GLWR, and TGW respectively while 24 QTNs were associated with more than one trait. Of these 160 QTNs, 73 were detected in two or more environments and were considered reliable QTLs for the respective traits. A total of 135 associated QTNs were annotated and located within the genes, including ABC transporter, Cytochrome450, Thioredoxin_M-type, and hypothetical proteins. Furthermore, the expression pattern of annotated QTNs demonstrated that only 122 were differentially expressed, suggesting these could potentially be related to seed development. The genomic regions/candidate genes for grain size traits identified in the present study represent valuable genomic resources that can potentially be utilized in the markers-assisted breeding programs to develop high-yielding varieties.

Multi-Trait Genome-Wide Association Studies of Sorghum bicolor Regarding Resistance to Anthracnose, Downy Mildew, Grain Mold and Head Smut.

Multivariate linear mixed models (mvLMMs) are widely applied for genome-wide association studies (GWAS) to detect genetic variants affecting multiple traits with correlations and/or different plant growth stages. Subsets of multiple sorghum populations, including the Sorghum Association Panel (SAP), the Sorghum Mini Core Collection and the Senegalese sorghum population, have been screened against various sorghum diseases such as anthracnose, downy mildew, grain mold and head smut. Still, these studies were generally performed in a univariate framework. In this study, we performed GWAS based on the principal components of defense-related multi-traits against the fungal diseases, identifying new potential SNPs (S04_51771351, S02_66200847, S09_47938177, S08_7370058, S03_72625166, S07_17951013, S04_66666642 and S08_51886715) associated with sorghum's defense against these diseases.

Fast integration and accumulation of beneficial breeding alleles through an AB–NAMIC strategy in wheat

Wheat (Triticum aestivum) is among the most important staple crops for safeguarding the food security of the growing world population. To bridge the gap between genebank diversity and breeding programs, we developed an advanced backcross–nested association mapping plus inter-crossed population (AB–NAMIC) by crossing three popular wheat cultivars as recurrent founders to 20 germplasm lines from a mini core collection. Selective backcrossing combined with selection against undesirable traits and extensive crossing within and between sub-populations created new opportunities to detect unknown genes and increase the frequency of beneficial alleles in the AB–NAMIC population. We performed phenotyping of 590 AB–NAMIC lines and a natural panel of 476 cultivars for six consecutive growing seasons and genotyped these 1066 lines with a 660K SNP array. Genome-wide association studies of both panels for plant development and yield traits demonstrated improved power to detect rare alleles and loci with medium genetic effects in AB–NAMIC. Notably, genome-wide association studies in AB–NAMIC detected the candidate gene TaSWEET6-7B (TraesCS7B03G1216700), which has high homology to the rice SWEET6b gene and exerts strong effects on adaptation and yield traits. The commercial release of two derived AB–NAMIC lines attests to its direct applicability in wheat improvement. Valuable information on genome-wide association study mapping, candidate genes, and their haplotypes for breeding traits are available through WheatGAB. Our research provides an excellent framework for fast-tracking exploration and accumulation of beneficial alleles stored in genebanks.

Evaluation and genetic variation of lutein content in Chinese common wheat

Selection of lutein-rich genotypes through breeding can enhance the nutritional value of wheat and provide a healthier diet. The present study used high performance liquid chromatography to analyze the lutein content of the Chinese wheat Mini Core Collection of 262 common wheats. In addition, the effects of water regime, accession type, release year, geographical origin, and the correlation of lutein content with various agronomic traits was examined. The lutein content among genotypes varied ten-fold, ranging from 0.87 to 8.90 μg/g. Ten cultivars with an average content more than 5.0 μg/g were identified as sources of the high lutein trait. Lutein content among different environments was significantly correlated and the genotype (G) and environment (E) response showed G > G × E > E with the effect of water level likely to be small. These results also demonstrated that the lutein content of Chinese wheat had not undergone extensive selection during the breeding process and was independent of accession type, plant habit, and grain color. However, lutein content was related to the geographical origin of accessions. Among ten agronomic traits evaluated, only grain related traits were associated with lutein content. These results provided essential information for breeding programs to improve the nutritional quality of wheat by enhancing lutein content.

Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses

Legume crops provide significant nutrition to humans as a source of protein, omega-3 fatty acids as well as specific macro and micronutrients. Additionally, legumes improve the cropping environment by replenishing the soil nitrogen content. Chickpeas are the second most significant staple legume food crop worldwide behind dry bean which contains 17%–24% protein, 41%–51% carbohydrate, and other important essential minerals, vitamins, dietary fiber, folate, β-carotene, anti-oxidants, micronutrients (phosphorus, calcium, magnesium, iron, and zinc) as well as linoleic and oleic unsaturated fatty acids. Despite these advantages, legumes are far behind cereals in terms of genetic improvement mainly due to far less effort, the bottlenecks of the narrow genetic base, and several biotic and abiotic factors in the scenario of changing climatic conditions. Measures are now called for beyond conventional breeding practices to strategically broadening of narrow genetic base utilizing chickpea wild relatives and improvement of cultivars through advanced breeding approaches with a focus on high yield productivity, biotic and abiotic stresses including climate resilience, and enhanced nutritional values. Desirable donors having such multiple traits have been identified using core and mini core collections from the cultivated gene pool and wild relatives of Chickpea. Several methods have been developed to address cross-species fertilization obstacles and to aid in inter-specific hybridization and introgression of the target gene sequences from wild Cicer species. Additionally, recent advances in “Omics” sciences along with high-throughput and precise phenotyping tools have made it easier to identify genes that regulate traits of interest. Next-generation sequencing technologies, whole-genome sequencing, transcriptomics, and differential genes expression profiling along with a plethora of novel techniques like single nucleotide polymorphism exploiting high-density genotyping by sequencing assays, simple sequence repeat markers, diversity array technology platform, and whole-genome re-sequencing technique led to the identification and development of QTLs and high-density trait mapping of the global chickpea germplasm. These altogether have helped in broadening the narrow genetic base of chickpeas.

Analysis of Physiological Variations and Genetic Architecture for Photosynthetic Capacity of Japanese Soybean Germplasm.

The culmination of conventional yield improving parameters has widened the margin between food demand and crop yield, leaving the potential yield productivity to be bridged by the manipulation of photosynthetic processes in plants. Efficient strategies to assess photosynthetic capacity in crops need to be developed to identify suitable targets that have the potential to improve photosynthetic efficiencies. Here, we assessed the photosynthetic capacity of the Japanese soybean mini core collection (GmJMC) using a newly developed high-throughput photosynthesis measurement system “MIC-100” to analyze physiological mechanisms and genetic architecture underpinning photosynthesis. K-means clustering of light-saturated photosynthesis (Asat) classified GmJMC accessions into four distinct clusters with Cluster2 comprised of highly photosynthesizing accessions. Genome-wide association analysis based on the variation of Asat revealed a significant association with a single nucleotide polymorphism (SNP) on chromosome 17. Among the candidate genes related to photosynthesis in the genomic region, variation in expression of a gene encoding G protein alpha subunit 1 (GPA1) showed a strong correlation (r = 0.72, p < 0.01) with that of Asat. Among GmJMC accessions, GmJMC47 was characterized by the highest Asat, stomatal conductance (gs), stomatal density (SDensity), electron transfer rate (ETR), and light use efficiency of photosystem II (Fv’/Fm′) and the lowest non-photochemical quenching [NPQ(t)], indicating that GmJMC47 has greater CO2 supply and efficient light-harvesting systems. These results provide strong evidence that exploration of plant germplasm is a useful strategy to unlock the potential of resource use efficiencies for photosynthesis.

GWAS and bulked segregant analysis reveal the Loci controlling growth habit-related traits in cultivated Peanut (Arachis hypogaea L.)

BackgroundPeanut (Arachis hypogaea L.) is a grain legume crop that originated from South America and is now grown around the world. Peanut growth habit affects the variety’s adaptability, planting patterns, mechanized harvesting, disease resistance, and yield. The objective of this study was to map the quantitative trait locus (QTL) associated with peanut growth habit-related traits by combining the genome-wide association analysis (GWAS) and bulked segregant analysis sequencing (BSA-seq) methods.ResultsGWAS was performed with 17,223 single nucleotide polymorphisms (SNPs) in 103 accessions of the U.S. mini core collection genotyped using an Affymetrix version 2.0 SNP array. With a total of 12,342 high-quality polymorphic SNPs, the 90 suggestive and significant SNPs associated with lateral branch angle (LBA), main stem height (MSH), lateral branch height (LBL), extent radius (ER), and the index of plant type (IOPT) were identified. These SNPs were distributed among 15 chromosomes. A total of 597 associated candidate genes may have important roles in biological processes, hormone signaling, growth, and development. BSA-seq coupled with specific length amplified fragment sequencing (SLAF-seq) method was used to find the association with LBA, an important trait of the peanut growth habit. A 4.08 Mb genomic region on B05 was associated with LBA. Based on the linkage disequilibrium (LD) decay distance, we narrowed down and confirmed the region within the 160 kb region (144,193,467–144,513,467) on B05. Four candidate genes in this region were involved in plant growth. The expression levels of Araip.E64SW detected by qRT-PCR showed significant difference between ‘Jihua 5’ and ‘M130’.ConclusionsIn this study, the SNP (AX-147,251,085 and AX-144,353,467) associated with LBA by GWAS was overlapped with the results in BSA-seq through combined analysis of GWAS and BSA-seq. Based on LD decay distance, the genome range related to LBA on B05 was shortened to 144,193,467–144,513,467. Three candidate genes related to F-box family proteins (Araip.E64SW, Araip.YG1LK, and Araip.JJ6RA) and one candidate gene related to PPP family proteins (Araip.YU281) may be involved in plant growth and development in this genome region. The expression analysis revealed that Araip.E64SW was involved in peanut growth habits. These candidate genes will provide molecular targets in marker-assisted selection for peanut growth habits.

Overview of developed core and mini core collections and their effective utilization in cultivated rice and its related species (Oryza sp.)—A review

AbstractGenus Oryza consists of two cultivated and 21 related wild species. Cultivated rice is not only the staple food of the majority of the countries in the world, but it also serves as a model crop for genomic studies. The rice germplasm is conserved in different gene banks around the world, which can be accessed for plant breeding programmes aiming to improve rice varieties. However, the ever‐increasing number of accessions poses problem of the phenotypic and genotypic characterization of the germplasm. Therefore, to speed up characterization and utilization of germplasm, the concept of core collection (~10–20% of total base collection) was developed which provides maximum diversity in limited number of accessions. Similarly, a mini core collection (~1–2% of the entire collection) is constructed retaining maximum diversity to provide wider genetic coverage in manageable numbers. The present review summarizes the current information on different core and mini core sets developed for varied purposes from world rice collections using different strategies.

Genome-Wide Association Studies of Plant Architecture-Related Traits in the Chinese Soybean Mini Core Collection

Plant architecture traits are closely related to plant biomass, lodging, and photosynthetic efficiency, which in turn affect soybean yield. In this study, we investigated a Chinese soybean mini core collection consisting of 224 germplasm accessions for four plant architecture-related traits (plant height (PH), number of nodes on main stem (NN), branch number (BN), and stem diameter (DI)) under three environments and conducted a genome-wide association study (GWAS) based on 1514 single nucleotide polymorphisms (SNPs). A total of 41 SNPs were found to be significantly associated with PH, NN, BN, and DI in two or more environments. Among these SNPs, 15 were located in regions in which plant architecture-related QTLs had been reported in previous studies, and 26 were new genetic loci. In addition, 18 potential candidate genes for plant architecture-related traits were obtained by predicting the genes in the interval of four large-effect markers (BARC-017097-02199, Map-2213, BARC-014639-01604, and Map-2223). This research will help to illuminate the genetic basis of soybean plant architecture-related traits and accelerate the process of plant architecture breeding by molecular marker-assisted selection in soybean.

Pin-by-Pin Coupled Transient Monte Carlo Analysis Using the iMC Code

In this article, we present a coupled multi-physics Monte Carlo reactor transient analysis framework implemented in the KAIST Monte Carlo iMC code. In the multi-physics framework, the time-dependent neutron transport calculation and the transient heat transfer analysis are done based on the predictor–corrector quasi-static Monte Carlo method and the three-dimensional finite element method, respectively. Using this high-fidelity analysis framework, we demonstrated the negative temperature feedback effect in two pressurized water reactor (PWR) transient scenarios. First, a 3-D burnable absorber-loaded fuel assembly was considered with all reflective boundary conditions. In this simple problem, a positive reactivity-induced transient was analyzed to characterize the reactor responses in view of the pin-wise power and temperature distribution. Second, the iMC multi-physics analysis is applied to a control rod withdrawal transient in the TMI-1 mini core problem, and detailed time-dependent results were provided and compared with the Serpent/SUBCHANFLOW analysis. In both cases, independent MC runs were performed to quantify the uncertainty of the multi-physics MC transient analysis.

Genome-wide association mapping identifies an SNF4 ortholog that impacts biomass and sugar yield in sorghum and sugarcane.

Sorghum is a feed/industrial crop in developed countries and a staple food elsewhere in the world. This study evaluated the sorghum mini core collection for days to 50% flowering (DF), biomass, plant height (PH), soluble solid content (SSC), and juice weight (JW), and the sorghum reference set for DF and PH, in 7-12 testing environments. We also performed genome-wide association mapping with 6 094 317 and 265 500 single nucleotide polymorphism markers in the mini core collection and the reference set, respectively. In the mini core panel we identified three quantitative trait loci for DF, two for JW, one for PH, and one for biomass. In the reference set panel we identified another quantitative trait locus for PH on chromosome 6 that was also associated with biomass, DF, JW, and SSC in the mini core panel. Transgenic studies of three genes selected from the locus revealed that Sobic.006G061100 (SbSNF4-2) increased biomass, SSC, JW, and PH when overexpressed in both sorghum and sugarcane, and delayed flowering in transgenic sorghum. SbSNF4-2 encodes a γ subunit of the evolutionarily conserved AMPK/SNF1/SnRK1 heterotrimeric complexes. SbSNF4-2 and its orthologs will be valuable in genetic enhancement of biomass and sugar yield in plants.

Mini Core Germplasm Collections for Developing Climate Resilient Crop Cultivars and Achieving Enhanced Genetic Gains in Plant Breeding Programs

Crop germplasm diversity contributes to developing improved crop cultivars aimed at increasing crop productivity to meet future food security needs of world. The large size of germplasm collections and lack of reliable information on traits of economic importance has resulted in low use (<1%) of germplasm. To facilitate realization of the potential benefits of germplasm collections to broaden the genetic base of cultivars in many crops, the mini core (~1% of the entire collection) concept was postulated and a development process proposed, to produce resources recognized globally as an “International Public Good” (IPG). Mini core collections have been developed in several crops and new diverse sources of genetic variation identified for biotic and abiotic stresses, agronomic and nutritional traits for use in crop improvement programs. Using genetically diverse sources scientists have developed breeding lines with enhanced trait expression and higher genetic gains. Molecular characterization of germplasm has revealed that phenotypic traits were as effective as molecular markers in sampling allelic diversity to form mini core collections.