Mini Core Research Articles

Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers.

In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.

Genome-Wide Association Mapping Identifies Novel Panicle Morphology Loci and Candidate Genes in Sorghum.

Panicle morphology is an important trait in racial classification and can determine grain yield and other agronomic traits in sorghum. In this study, we performed association mapping of panicle length, panicle width, panicle compactness, and peduncle recurving in the sorghum mini core panel measured in multiple environments with 6,094,317 single nucleotide polymorphism (SNP) markers. We mapped one locus each on chromosomes 7 and 9 to recurving peduncles and eight loci for panicle length, panicle width, and panicle compactness. Because panicle length was positively correlated with panicle width, all loci for panicle length and width were colocalized. Among the eight loci, two each were on chromosomes 1, 2, and 6, and one each on chromosomes 8 and 10. The two loci on chromosome 2, i.e., Pm 2-1 and Pm 2-2, were detected in 7 and 5 out of 11 testing environments, respectively. Pm 2-2 colocalized with panicle compactness. Candidate genes were identified from both loci. The rice Erect Panicle2 (EP2) ortholog was among the candidate genes in Pm 2-2. EP2 regulates panicle erectness and panicle length in rice and encodes a novel plant-specific protein with unknown functions. The results of this study may facilitate the molecular identification of panicle morphology-related genes and the enhancement of yield and adaptation in sorghum.

Genetic diversity analysis in a mini core collection of Damask rose (Rosa damascena Mill.) germplasm from Iran using URP and SCoT markers

BackgroundRosa damascena Mill is a well-known species of the rose family. It is famous for its essential oil content. The aim of the present study was to assess the genetic diversity and population structure of a mini core collection of the Iranian Damask rose germplasm. This involved the use of universal rice primers (URP) and start codon targeted (SCoT) molecular markers. ResultsFourteen URP and twelve SCoT primers amplified 268 and 216 loci, with an average of 19.21 and 18.18 polymorphic fragments per primer, respectively. The polymorphic information content for URR and SCoT primers ranged from 0.38 to 0.48 and 0.11 to 0.45, with the resolving power ranging from 8.75 to 13.05 and 9.9 to 14.59, respectively. Clustering was based on neighbor-joining (NJ). The mini core collection contained 40 accessions and was divided into three distinct clusters, centered on both markers and on the combination of data. ConclusionCluster analysis and principal coordinate analysis were consistent with genetic relationships derived by STRUCTURE analysis. The findings showed that patterns of grouping did not correlate with geographical origin. Both molecular markers demonstrated that the accessions were not genetically diverse as expected, thereby highlighting the possibility that gene flow occurred between populations.

Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice

BackgroundCadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity.ResultsIn this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs.ConclusionThe exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

Identification of Single Nucleotide Polymorphism in TaSBEIII and Development of KASP Marker Associated With Grain Weight in Wheat

Manipulation of genes involved in starch synthesis could significantly affect wheat grain weight and yield. The starch-branching enzyme (SBE) catalyzes the formation of branch points by cleaving the α-1,4 linkage in polyglucans and reattaching the chain via an α-1,6 linkage. Three types of SBE isoforms (SBEI, SBEII, and SBEIII) exist in higher plants, with the number of SBE isoforms being species-specific. In this study, the coding sequence of the wheat TaSBEIII gene was amplified. After the multiple sequence alignment of TaSBEIII genome from 20 accessions in a wheat diversity panel, one SNP was observed in TaSBEIII-A, which formed the allelic marker allele-T. Based on this SNP at 294 bp (C/T), a KASP molecular marker was developed to distinguish allelic variation among the wheat genotypes for thousand grain weight (TGW). The results were validated using 262 accessions of mini core collection (MCC) from China, 153 from Pakistan, 53 from CIMMYT, and 17 diploid and 18 tetraploid genotypes. Association analysis between TaSBEIII-A allelic variation and agronomic traits found that TaSBEIII-A was associated with TGW in mini core collection of China (MCC). The accessions possessing Allele-T had higher TGW than those possessing Allele-C; thus, Allele-T was a favorable allelic variation. By analyzing the frequency of the favorable allelic variation Allele-T in MCC, it increased from pre-1950 (25%) to the 1960s (45%) and increased continuously from 1960 to 1990 (80%). The results suggested that the KASP markers can be utilized in grain weight improvement, which ultimately improves wheat yield by marker-assisted selection in wheat breeding. The favorable allelic variation allele-T should be valuable in enhancing grain yield by improving the source and sink simultaneously. Furthermore, the newly developed KASP marker validated in different genetic backgrounds could be integrated into a breeding kit for screening high TGW wheat.

Genetic Dissection of Seedling Root System Architectural Traits in a Diverse Panel of Hexaploid Wheat through Multi-Locus Genome-Wide Association Mapping for Improving Drought Tolerance.

Cultivars with efficient root systems play a major role in enhancing resource use efficiency, particularly water absorption, and thus in drought tolerance. In this study, a diverse wheat association panel of 136 wheat accessions including mini core subset was genotyped using Axiom 35k Breeders’ Array to identify genomic regions associated with seedling stage root architecture and shoot traits using multi-locus genome-wide association studies (ML-GWAS). The association panel revealed a wide variation of 1.5- to 50-fold and were grouped into six clusters based on 15 traits. Six different ML-GWAS models revealed 456 significant quantitative trait nucleotides (QTNs) for various traits with phenotypic variance in the range of 0.12–38.60%. Of these, 87 QTNs were repeatedly detected by two or more models and were considered reliable genomic regions for the respective traits. Among these QTNs, eleven were associated with average diameter and nine each for second order lateral root number (SOLRN), root volume (RV) and root length density (RLD). A total of eleven genomic regions were pleiotropic and each controlled two or three traits. Some important candidate genes such as Formin homology 1, Ubiquitin-like domain superfamily and ATP-dependent 6-phosphofructokinase were identified from the associated genomic regions. The genomic regions/genes identified in this study could potentially be targeted for improving root traits and drought tolerance in wheat.

Variation for Photoperiod and Temperature Sensitivity in the Global Mini Core Collection of Sorghum.

Information on photoperiod and temperature sensitivity of sorghum germplasm is important to identify appropriate sources for developing cultivars with a broad adaptation. The sorghum mini core collection consisting of 242 accessions along with three control cultivars were evaluated for days to 50% flowering (DFL) and plant height in two long-day rainy and two short-day post-rainy seasons, and for grain yield and 100-seed weight in the two post-rainy seasons. Differences in DFL and cumulative growing degree days (CGDD) in the rainy and post-rainy seasons were used to classify the accessions for photoperiod and temperature sensitivity. Results revealed 18 mini core landraces as photoperiod and temperature insensitive (PTINS), 205 as photoperiod sensitive and temperature insensitive (PSTINS), and 19 as photoperiod and temperature-sensitive (PTS) sources. The 19 PTS sources and 80 PSTINS sources took less DFL in the long-day rainy seasons than in the short-day post-rainy season indicating their adaptation to the rainy season and a possible different mechanism than that trigger flowering in the short-day sorghums. In all three groups, several accessions with desirable combinations of agronomic traits were identified for use in the breeding programs to develop climate-resilient cultivars and for genomic studies to identify genes responsible for the photoperiod and temperature responses.

Identification and development of a KASP functional marker of TaTAP46‐5A associated with kernel weight in wheat (Triticum aestivum)

AbstractTAP46 (Type 2A‐phosphatase‐Associated Protein 46 kDa) is homologous to yeast TAP42 or the animal α4 gene and is a crucial gene in the target of rapamycin regulation of protein phosphatase 2A. It has been proven to influence the thousand‐kernel weight (TKW) and kernel size in transgenic wheat. To rapidly identify high‐yield wheat germplasms of TaTAP46, four interlinked single nucleotide polymorphisms were identified by resequencing the TaTAP46‐5A gene in 32 varieties, forming two haplotypes: Hap1 and Hap2. A KASP marker, −1462A/C, was developed to identify Hap1/Hap2. A 157 Chinese wheat mini core collection and 348 Chinese modern collection were constructed for association analysis of the two haplotypes and their phenotypes. The results showed that the Hap1/Hap2 of TaTAP46‐5A was significantly associated with the TKW and kernel size. Hap1 was a favourable haplotype with higher TKW and larger kernel size compared to those of Hap2. Hap1 is a stable high yield type of the TaTAP46 gene that has been continuously selected in high‐yield wheat breeding worldwide. The germplasm of Hap1 can be selected quickly using the KASP primer −1462A/C, to improve breeding efficiency.

Genome-wide association analysis for yield-related traits at the R6 stage in a Chinese soybean mini core collection.

Soybean (Glycine max (L.) Merr.) is an economically important crop for vegetable oil and protein production, and yield is a critical trait for grain/vegetable uses of soybean. However, our knowledge of the genes controlling the vegetable soybean yield remains limited. To better understand the genetic basis of the vegetable soybean yield. The 100-pod fresh weight (PFW), 100-seed fresh weight (SFW), kernel percent (KP) and moisture content of fresh seeds (MCFS) at the R6 stage are four yield-related traits for vegetable soybean. We investigated a soybean mini core collection composed of 224 germplasm accessions for four yield-related traits in two consecutive years. Based on 1514 single nucleotide polymorphisms (SNPs), genome-wide association studies (GWAS) were conducted using a mixed linear model (MLM). Extensive phenotypic variation existed in the soybean mini core collection and significant positive correlations were shown among most of traits. A total of 16 SNP markers for PFW, SFW, KP and MCFS were detected in all environments via GWAS. Nine SNP markers were repeatedly identified in two environments. Among these markers, eight were located in or near regions where yield-related QTLs have been reported in previous studies, and one was a novel genetic locus identified in this study. In addition, we conducted candidate gene analysis to the large-effect SNP markers, a total of twelve genes were proposed as potential candidate genes of soybean yield at the R6 stage. These results will be beneficial for understanding the genetic basis of soybean yield at the R6 stage and facilitating the pyramiding of favourable alleles for future high-yield breeding by marker-assisted selection in vegetable soybean.

Genotype × Environment Interaction for Resistance to Early Leaf Spot of Groundnut Mini Core Collections in the Savannas of Nigeria

Background: The genetic yield potential of groundnut (Arachis hypogaea L.) has been continuously challenged by several diseases including early leaf spot (ELS).Methods: In the current study, we evaluated groundnut mini core collections under artificial and natural disease epiphytotics in six environments to identify stable elite sources for ELS resistance and pod yield. Mixed model analysis was done to adequately capture the variance component as a result of genotype (G), environment (E) and G × E interaction (GEI).Result: Highly significant (p less than 0.001) effects for G and GEI on ELS and pod weight were observed. The parametric and non-parametric stability models ranked the genotype differently for their stability to ELS. The GGE biplot identified ICG 1519 as a stable genotype for the ELS resistance. For pod weight, ICG 8896 and ICG 7897 were consistently stable from all the stability models including the GGE biplot. ICG 9449 and ICG 4540 were identified as stable genotypes for both ELS and pod weight. These elite sources of ELS resistance identified in the current study will be useful in the development and deployment of groundnut varieties with resistance to ELS and high pod yielding potentials.

Assessment of root phenotypes in mungbean mini-core collection (MMC) from the World Vegetable Center (AVRDC) Taiwan.

Mungbean (Vigna radiata L.) is an important food grain legume, but its production capacity is threatened by global warming, which can intensify plant stress and limit future production. Identifying new variation of key root traits in mungbean will provide the basis for breeding lines with effective root characteristics for improved water uptake to mitigate heat and drought stress. The AVRDC mungbean mini core collection consisting of 296 genotypes was screened under modified semi-hydroponic screening conditions to determine the variation for fourteen root-related traits. The AVRDC mungbean mini core collection displayed wide variations for the primary root length, total surface area, and total root length, and based on agglomerative hierarchical clustering eight homogeneous groups displaying different root traits could be identified. Germplasm with potentially favorable root traits has been identified for further studies to identify the donor genotypes for breeding cultivars with enhanced adaptation to water-deficit stress and other stress conditions.

Genetic diversity and population structure analysis – a prerequisite for constructing a mini core collection of Balkan Capsicum annuum germplasm

Pepper (Capsicum annuum L.) is one of the most important vegetable crops worldwide. The Balkans, including Bulgaria, are considered as the secondary centre of pepper diversity especially for C. annuum, where local forms with diverse phenotypes and qualities have formed due to the specific agro-climatic conditions and breeding traditions. Evaluation of the genetic diversity and structure of a pepper collection is an important tool for further development of new varieties and the maintenance of sustainable agriculture. In this study, a set of 179 C. annuum accessions collected from different locations in the Balkan Peninsula was genotyped with 21 simple sequence repeat (SSR; microsatellite) markers. In total, 146 alleles were amplified among which the majority were with low frequencies (<5%). The mean He, Ho and PIC for the 21 SSR loci in the whole set were 0.531, 0.249 and 0.483, respectively. Model-based structure analysis divided the collection into 3 main clusters (K = 3) that grouped accessions with distinct fruit traits like shape, size, pungency. Further genetic structure analysis at increasing Ks suggested the presence of sub-clustering within the three main clusters. A Balkan C. annuum mini core collection was constructed based on the allelic diversity and the inferred genetic structure. As far as the mini core collection captured substantial part of the allele richness, genetic and phenotypic diversity of the analysed 176 non-redundant accessions, while maintaining good representativeness, we believe it will be of high interest to pepper breeders and germplasm conservation specialists. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1946428 .

HIGH-FIDELITY MULTI-PHYSICS PIN-BY-PIN MODEL OF A SVEA-96 OPTIMA2 ASSEMBLY WITH TORT-TD/CTF

This paper describes the development of a 3-d high-fidelity multi-physics pin-by-pin neu-tronic and sub-channel thermal hydraulic model of a SVEA-96 Optima2 fuel assembly for the coupled code system TORT-TD/CTF. No pin power reconstruction is applied. Detailed descriptions are given on (a) the generation of few-group parameterized pin cell-homogenized cross section data using HELIOS, (b) the 3-d neutronic pin-by-pin and ther-mal-hydraulic sub-channel model of a single SVEA-96 Optima2 assembly and its qualifica-tion by Monte Carlo models using Serpent, (c) coupled steady-state results for a single as-sembly and (d) coupled steady-state and transient simulations of a 4-by-4 mini core model of SVEA-96 Optima2 assemblies in a partially rodded state.

Identification of Blast Resistant Genotypes among Drought Tolerant Finger Millet in Uganda

Finger millet is an important food security crop among many subsistence farmers living in marginal and especially semi-arid regions of Eastern Africa. However, crop production is affected mainly by terminal drought and blast disease caused by fungus Pyricularia grisea. Both collectively lead to over 90% grain yield loss depending on environmental conditions, cropping systems and varietal differences. Therefore, resistance breakdown remains high owing to variability in the blast pathogen and weather conditions. Stable varieties should possess both blast resistance and drought. In order to initiate breeding for multiple resistance to blast on drought-tolerant background, a study was conducted to identify variability for blast resistance from adapted germplasm as an initial step in developing a breeding strategy for incorporating resistance. Thirty genotypes from drought-prone agro-ecologies and including mini core germplasm from NARO-NaSARRI national Finger Millet improvement programme were assessed. They were screened using a local virulent pathogen isolate (NGR1) from Ngora, representing Teso major farming system and is a hot spot for the blast. The screening was under controlled conditions from in Makerere University Agricultural Research Institute (MUARIK) in 2012b. The results showed significance (p&lt;0.01) for Area Under Disease Progressive Curve (AUDPC). Subsequently, the study identified IE927, Seremi1, Seremi3, Sec220 and Kabale as highly resistant to foliar blast infection comparable to Gulu-E a standard broad-spectrum resistant check and they could be used to improve finger millet for blast resistance. Meanwhile DR33, IE9 and IE2576 as most susceptible compared to non-race -specific susceptible check E11 from Uganda.

Identification of potential QTLs and genes associated with seed composition traits in peanut (Arachis hypogaea L.) using GWAS and RNA-Seq analysis

Cultivated peanut (Arachis hypogaea L.) is a major oilseed crop providing edible oil and protein. Oil quality is determined by fatty acid composition including the ratio of oleic acid (C18:1) and linoleic acid (C18:2). A genome-wide association study with 13,382 single nucleotide polymorphisms (SNPs) was conducted to investigate the genetics basis of oil, protein, eight fatty acid concentrations, and O/L ratio (ratio of oleic and linoleic acid) using a diverse panel of 120 genotypes mainly selected from the U.S. peanut mini core collection grown in two years. A total of 178 significant quantitative trait loci (QTLs) associated with those seed composition traits were identified with phenotypic variation explained (PVE) from 18.35% to 27.56%. RNA-Seq analysis identified 282 DEGs (differentially expressed genes) within the 1Mb of the significant QTLs for seed composition traits. Among those 282 genes, sixteen candidate genes for seed fatty acid metabolism and protein synthesis were screened according to the gene functions.

Genome-wide association studies of ionomic and agronomic traits in USDA mini core collection of rice and comparative analyses of different mapping methods

BackgroundRice is an important human staple food vulnerable to heavy metal contamination leading to serious concerns. High yield with low heavy metal contamination is a common but highly challenging goal for rice breeders worldwide due to lack of genetic knowledge and markers.ResultsTo identify candidate QTLs and develop molecular markers for rice yield and heavy metal content, a total of 191 accessions from the USDA Rice mini-core collection with over 3.2 million SNPs were employed to investigate the QTLs. Sixteen ionomic and thirteen agronomic traits were analyzed utilizing two univariate (GLM and MLM) and two multivariate (MLMM and FarmCPU) GWAS methods. 106, 47, and 97 QTLs were identified for ionomics flooded, ionomics unflooded, and agronomic traits, respectively, with the criterium of p-value < 1.53 × 10− 8, which was determined by the Bonferroni correction for p-value of 0.05. While 49 (~ 20%) of the 250 QTLs were coinciding with previously reported QTLs/genes, about 201 (~ 80%) were new. In addition, several new candidate genes involved in ionomic and agronomic traits control were identified by analyzing the DNA sequence, gene expression, and the homologs of the QTL regions. Our results further showed that each of the four GWAS methods can identify unique as well as common QTLs, suggesting that using multiple GWAS methods can complement each other in QTL identification, especially by combining univariate and multivariate methods.ConclusionsWhile 49 previously reported QTLs/genes were rediscovered, over 200 new QTLs for ionomic and agronomic traits were found in the rice genome. Moreover, multiple new candidate genes for agronomic and ionomic traits were identified. This research provides novel insights into the genetic basis of both ionomic and agronomic variations in rice, establishing the foundation for marker development in breeding and further investigation on reducing heavy-metal contamination and improving crop yields. Finally, the comparative analysis of the GWAS methods showed that each method has unique features and different methods can complement each other.

Association of molecular markers with physio-biochemical traits related to seed vigour in rice.

Eighteen physio-biochemical traits influencing seed vigour were studied for their association with molecular markers using a mini core set constituted from 120 germplasm lines. High genetic variation was detected in the parameters namely chlrophyll a, Chlrophyll b, total chlorophyll, carotenoids, total anthocyanin content, gamma-oryzanols, total phenolics content,superoxide dismutase, catalase, guaicol peroxidase, total soluble sugar, total protein, seed vigour index -I and seed vigour index -II. Strong positive correlation of seed vigour index II was observed with amylose content, total anthocyanin content, catalase, total phenolic content and total flavonoid content while a negative association was observed for gamma-oryzanol content. High gene diversity (0.7169) and informative markers value (0.6789) were estimated from the investigation. Three genetic structure groups were observed in the panel population and genotypes were grouped in the subpopulations based on the seed vigour trait. Differences in the fixation indices of the three sub populations indicated existence of linkage disequilibrium in the studied panel population. Association of the traits namely total flavonoids, superoxide dismutase, catalase, chlorophyll a, Chlorophyll b, total chlorophyll, carotenoids, starch, amylose, total anthocyanin, gamma-oryzanol, total phenolics with the molecular markers were detected by Generalized Linear Model and Mixed Linear Model showing > 0.10 R2 value. Association of the trait, total flavonoids with marker RM7364 located on chromosome 8 reported in earlier study was validated in this investigation. The validated markers and the novel markers detected showing higher R2 value will be useful for improvement of seed vigour in rice.

Principal component analysis for productivity and grain quality traits in rabi sorghum (Sorghum bicolor L. Moench)

Principal component analysis was carried out involving 24 selected mini core and 16 promising varieties during rabi sorghum. Principal component analysis revealed that, four out of twelve principal components with eigen values >1 were extracted. Among the selected mini core, three components contributed 66.37% of the total variation. Principal components first three contributed 30.55%, 19.74%, and 16.07% toward the variation, respectively. Plant height and true density traits contributed positively in mini core accessions. Whereas, among promising released varieties the three components contributed 66.46% of the total variation and first three contributed, 30.07%, 19.51% and 16.88%, respectively. Ear head width, 100 seed weight, seed volume, true density and seed size has showed positive contribution in all three principal components of variation observed in varieties. So, these characters spread over different principal component and contributing most to explain the variability should be taken into consideration for their utilization in breeding programme.

The MYB transcription factor TaPHR3-A1 is involved in phosphate signaling and governs yield-related traits in bread wheat.

Improved inorganic phosphate (Pi) use efficiency in crops will be important for sustainable agriculture. Exploring molecular mechanisms that regulate Pi uptake could provide useful information for breeding wheat with improved Pi use efficiency. Here, a TaPHR3-A1 (Gene ID: TraesCS7A02G415800) ortholog of rice OsPHR3 that functions in transcriptional regulation of Pi signaling was cloned from wheat chromosome 7A. Ectopic expression of TaPHR3-A1 in Arabidopsis and rice produced enhanced vegetative growth and more seeds. Overexpression in transgenic rice led to increased biomass, grain number, and primary panicle branching by 61.23, 42.12, and 36.34% compared with the wild type. Transgenic wheat lines with down-regulation of TaPHR3-A1 exhibited retarded growth and root hair development at the seedling stage, and showed yield-related effects at the adult stage when grown in both low- and sufficient Pi conditions, indicating that TaPHR3-A1 positively regulated tolerance to low Pi. Introgression lines further confirmed the effect of TaPHR3-A1 in improving grain number. The Chinese wheat mini core collection and a recombinant inbred line analysis demonstrated that the favorable allele TaPHR3-A1-A associated with higher grain number was positively selected in breeding. A TaPHR3-A1-derived cleaved amplified polymorphic sequence marker effectively identified haplotype TaPHR3-A1-A. Our results suggested that TaPHR3-A1 was a functional regulatory factor for Pi uptake and provided useful information for marker-assisted selection for high yield in wheat.

Evaluation of Glycine max and Glycine soja for Resistance to Calonectria ilicicola

Breeding for resistance to soybean red crown rot (Calonectria ilicicola) has long been hampered by the lack of genetic sources of adequate levels of resistance to use as parents. Mini core collections of soybean (Glycine max) originating from Japan (79 accessions), from around the world (80 accessions), and a collection of wild soybeans (Glycine soja) consisting 54 accessions were evaluated for resistance to C. ilicicola (isolate UH2-1). In the first two sets, average disease severity scores of 4.2 ± 0.28 and 4.6 ± 0.31 on a rating scale from zero for no symptom to 5.0 for seedling death were recorded from the set from Japan and the world. No high levels of resistance were observed in these two sets. On the other hand, disease severity score of 3.8 ± 0.35 for the wild soybean accessions was somewhat lower and exhibited higher levels of resistance compared to the soybean cultivars. Three accessions in the wild soybean collection (Gs-7, Gs-9, and Gs-27) had disease severity score ≤2.5 and showed &gt;70% reduction in fungal growth in the roots compared to soybean control cv. “Enrei”. Further analysis using 10 C. ilicicola isolates revealed that accession Gs-9 overall had a wide range of resistance to all isolates tested, with 37% to 93% reduction in fungal growth relative to the cv. Enrei. These highly resistant wild soybean lines may serve as valuable genetic resources for developing C. ilicicola-resistant soybean cultivars.