Set Of Germplasm Research Articles

Uncovering candidate genes involved in photosynthetic capacity using unexplored genetic variation in Spring Wheat.

SummaryTo feed an ever‐increasing population we must leverage advances in genomics and phenotyping to harness the variation in wheat breeding populations for traits like photosynthetic capacity which remains unoptimized. Here we survey a diverse set of wheat germplasm containing elite, introgression and synthetic derivative lines uncovering previously uncharacterized variation. We demonstrate how strategic integration of exotic material alleviates the D genome genetic bottleneck in wheat, increasing SNP rate by 62% largely due to Ae. tauschii synthetic wheat donors. Across the panel, 67% of the Ae. tauschii donor genome is represented as introgressions in elite backgrounds. We show how observed genetic variation together with hyperspectral reflectance data can be used to identify candidate genes for traits relating to photosynthetic capacity using association analysis. This demonstrates the value of genomic methods in uncovering hidden variation in wheat and how that variation can assist breeding efforts and increase our understanding of complex traits.

Analysis of the primary sources of quantitative adult plant resistance to stripe rust in U.S. soft red winter wheat germplasm.

Stripe rust, or yellow rust (Puccinia striiformis Westend. f. sp. tritic), is a disease of wheat (Triticum aestivum L.) historically causing significant economic losses in cooler growing regions. Novel isolates of stripe rust with increased tolerance for high temperatures were detected in the United States circa 2000. This increased heat tolerance puts geographic regions, such as the soft red winter wheat (SRWW) growing region of the southeastern United States, at greater risk of stripe rust induced losses. In order to identify sources of stripe rust resistance in contemporary germplasm, we conducted genome-wide association (GWA) studies on stripe rust severity measured in two panels. The first consisted of 273 older varieties, landraces, and some modern elite breeding lines and was evaluated in environments in the U.S. Pacific Northwest and the southeastern United States. The second panel consisted of 588 modern, elite SRWW breeding lines and was evaluated in four environments in Arkansas and Georgia. The analyses identified three major resistance loci on chromosomes: 2AS (presumably the 2NS:2AS alien introgression from Aegilops ventricosa Tausch; syn. Ae. caudata L.), 3BS, and 4BL. The 4BL locus explained a greater portion of variance in resistance than either the 2AS or 3BS loci in southeastern environments. However, its effects were unstable across different environments and sets of germplasm, possibly a result of its involvement in epistatic interactions. Relatively few lines carry resistance alleles at all three loci, suggesting that there is a pre-existing reservoir of enhanced stripe rust resistance that may be further exploited by regional breeding programs.

Identification of inhibitors of pinellic acid generation in whole wheat bread

Bitterness is a common aversive flavor attribute of foods associated with low consumer acceptance. Untargeted LC–MS flavoromic profiling was utilized to identify endogenous compounds that influence the generation of the bitter compound 9,12,13-trihydroxy-trans-10-octadecenoic acid (pinellic acid) during bread making. A diverse sample set of wheat germplasm was chemically profiled. The corresponding pinellic acid concentrations after dough formation were modeled by orthogonal partial least squares (OPLS) with good fit (R2Y = 0.8) and predictive ability (Q2 = 0.6). The most predictive feature (negatively correlated), postulated to interfere with the biosynthetic pathway, was identified as schaftoside, an apigenin di-C-glycoside. Recombination experiments involving the addition of schaftoside to flour prior to breadmaking resulted in a 26% decrease in pinellic acid formation and significantly lower perceived bitterness intensity in whole wheat bread. This work provides novel understanding of bitter generation pathways in wheat products and new strategies to improve flavor profiles and consumer acceptability.

Genetic Diversity of Gora Rice (Oryza sativa L.) Landraces of Chotanagpur Plateau Region in Eastern India

The rice cultivars grown in the uplands of the state of Jharkhand, India are traditionally known as gora rice. These cultivars possess many important traits such as high seedling vigour, deeper roots and drought tolerance. In this study, a collection of gora landraces were assessed for morpho-genetic diversity using SSR markers. Morpho-agronomic analysis indicated that although seed morphological features are traditionally used for differentiating landraces, based on overall morpho-agronomic features also the cultivars could be differentiated as found in case of black gora. A genetic diversity analysis using 39 SSR markers detected considerable gene diversity (0.52) within gora cultivars. The white gora accessions were classified as indica, and rest including black gora, brown gora and other gora accessions belonged to aus group. This germplasm set provides scope for further genetic studies on multiple abiotic stress tolerance traits such as drought, submergenece and phosphorus starvation and traits for aerobic adaptation.

Agronomic Performance and Genotype × Moisture Conditions Interaction for Morpho-Physiological Traits in Durum Wheat

Fourteen promising durum wheat lines, representing the elite durum germplasm for rainfed conditions, along with three check cultivars were assessed under drought and irrigated conditions for three growing seasons. The main objectives were to (i) evaluate the agronomic performance of durum wheat genotypes under different moisture stress conditions (mild, moderate, severe) and (ii) investigate the traits significantly contributing to drought tolerance. Combined ANOVA across environments for grain yield and the traits studied showed significant differences (P < 0.01) for genotype, year, moisture condition, year × moisture condition, genotype × year, and genotype × moisture condition interactions. There were differences in trait associations across the years and moisture conditions showing that the traits were significantly affected by the year and moisture conditions effects. Heading date, plant height, spike length and SPAD-reading with low ratio of σ2ge/σ2g showed a high value for heritability. Genotypes showed specific adaptation to different environmental condition as supported by significant (P < 0.01) for genotype × moisture condition interaction. Heading date, peduncle extrusion, plant height, days to maturity and 1000-kernel weight with lower genotype × moisture interaction than grain yield, were the traits contributing the most to drought tolerance. It is concluded that these traits could aid in the selection of durum wheat subject to moderate and severe stress, particularly in early generations. Under severe water stress condition, earliness to heading was an important drought escape mechanism, but inherent drought tolerance could be inferred from responses of a few genotypes. To determine effects of GE interaction on grain yield, data were subjected to GGE biplot analysis, which identified breeding lines G16, G12, G15 and G10 as the most stable and high yielding genotypes across different moisture stress conditions that can be used in convergent durum breeding program to develop drought tolerant varieties. The breeding lines which out-yielded the check cultivars are the stand out as the best promising germplasm but present different sets of favorable traits under stressed or favorable conditions.

Optimizing a Seedling Screening Method for Anthracnose Resistance in Watermelon

Among three races of Colletotrichum orbiculare, which cause anthracnose of cucurbits, screening for race 2 resistance was studied under greenhouse conditions at various inoculum concentrations, and plants were rated on different days postinoculation (DPI). The objectives of this study were optimizing inoculum concentration and phenotyping DPI for seedling resistance. Five inoculum concentrations were compared (2.5 × 104, 5 × 104, 1 × 105, 2.5 × 105, and 5 × 105conidial spores/ml). Four watermelon genotypes (‘Black Diamond’, ‘Charleston Gray 133’, PI 543210, and PI 189225) and two cucumber genotypes (‘Marketer’ and ‘H19 Little Leaf’) were evaluated. Disease was recorded on the percentage of cotyledon area lesion, severity of hypocotyl lesion (SHL), severity of petiole lesion (SPL), and percentage of leaf area lesion (PLL), as well as a disease index (INDX) from 5 to 14 DPI. There was a significant difference among genotypes and inoculum concentrations. The resistant PI 189225 was significantly different (P &lt; 0.05) from the highly susceptible PI 543210. Inoculum 1 × 105spores/ml was at par with 5 × 105and 2.5 × 105but significantly different from 5 × 104and 2.5 × 104for AUDPS PLL, AUDPS INDX, AUDPS SPL, and AUDPS SHL. Inoculum at 1 × 105spores/ml was optimal to differentiate germplasm. A genotype plus genotype-by-environment biplot showed that PLL was a representative rating. A single PLL rating on 9 DPI would optimize resources for screening a large set of germplasm for anthracnose resistance in a watermelon breeding program.

Genetic diversity of walnut (Juglans regia L.) seedlings through SSR markers in north-western Himalayan region of Jammu

screening of 25 SSR markers, revealed 23 clear and consistent amplification profiles in the entire walnut germplasm set. A total of 54 alleles were amplified by SSR primers and the number of alleles range from 2 to 3. The PIC value ranged from 0.36 to 0.68. The dendrogram classified all genotypes into two main clusters with various degrees of subclustering. Estimated genetic dissimilarity coefficient ranged from 0.36 to 0.85. Through model-based cluster analysis all genotypes were grouped into 5 genetically distinct subpopulations. The expected heterozygosity at a given locus was found to range from 0.520 to 0.5477. Similarly, population differentiation measurements (Fst) ranged from 0.2286 to 0.2909. These findings would be helpful for decision making in future walnut breeding studies, germplasm management activities to maximize genetic diversity in walnut germplasm and may also prove useful in future for conducting association mapping in walnut for different traits.

Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers.

Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.

Characterization of wheat germplasm conserved in the Indian National Genebank and establishment of a composite core collection

AbstractThe use of untapped plant genetic resources of wheat (Triticum spp.) can enhance its productivity. In the present study, we characterized 22,416 accessions of three different species of wheat conserved in the Indian National Genebank using 23 qualitative and 12 quantitative traits to develop a core set. These accessions were highly diverse on the basis of range, coefficient of variation, and Shannon–Weaver diversity index. Initial grouping was done on the bases of species and origin, and thereafter, agromorphological data were used to develop core sets for each species group using the heuristic approach with PowerCore. Finally, a composite core set was constituted comprising 2,226 accessions, which included 1,779 accessions of bread wheat (T. aestivum L.), 394 of durum wheat [T. turgidum L. subsp. durum (Desf.) van Slageren], and 53 of emmer wheat [T. dicoccon Schrank; syn. T. turgidum L. subsp. dicoccon (Schrank) Thell]. The core set was validated under field conditions. Also, the coincidence rate of range (CR) (bread wheat, 85.78%; durum wheat, 87.52%; and emmer wheat, 95.34%) and variable rate of the coefficient of variation (VR) (bread wheat, 174.9%; durum wheat, 136.5%; and emmer wheat, 105.81%) were more than the threshold values of 80 and 100%, respectively. The phenotypic correlations among different traits attributable to coadapted gene complexes and total variation shown by principal components in the entire set were also mostly preserved in the core set. The composite wheat core and the trait‐specific germplasm sets identified would serve as valuable resources for global wheat improvement programs.

Comprehensive Analysis of Different Contemporary Barley Genotypes Enhances and Expands the Scope of Barley Contributions to Beer Flavor

Recent research has demonstrated contributions of barley genotype to beer flavor based on the progeny of a cross between an heirloom and a more contemporary barley variety. To advance this line of research, the current study used two independent sets of barley germplasm to address the contributions of different barley genotypes to beer flavor. Pedigree, quality of malt and beer, and beer metabolomic profiles were compared within and between the two sets. Utilizing both laboratory and consumer panels, differences in sensory attributes of malt hot steeps and lager beers that are attributable to barley genotype were investigated. Genotype, in this context, is defined in the broadest sense to include experimental germplasm and released varieties. Results concur with previous studies: the two sets of barley germplasm were found to have, both within and between, distinct but subtle differences in flavor profiles of malt hot steeps and finished lager beers. Distinct metabolomic profiles, attributable to barley genotype, were detected. Further, covariation of metabolomic profiles and sensory attributes were identified using data from both sensory panels. These observations lead to the conclusion that the variable metabolites observed among the two sets of barley germplasm are a direct result of genetic differences that lead to differential chemical responses within the malting and brewing processes.

Identification of new resistant sources against downy mildew disease from a selected set of cucumber germplasm and its wild relatives

This study was undertaken to identify new sources of resistance against downy mildew of cucumber caused by Pseudoperonospora cubensis [(Berk. and Cart.) Rostow]. Pot experiments were conducted with 16 accessions each of Cucumis sativus and C. hardwickii during the years 2017 and 2018 using 12 isolates of P. cubensis representing different agroclimatic zones of India. The accession, IC331627 from Dehradun, Uttarakhand showed plant disease index (PDI) ranging from 5.55-20.35 per cent with an average PDI of 11.56 and 11.87 per cent during the years, 2017 and 2018, respectively. Hence, IC331627 was identified to be resistant against the five isolates of P. cubesis (Pc12, Pc17, Pc19, Pc21 and Pc24) and moderately resistant against one isolate (Pc22). This resistant accession C. hardwickii (IC331627) could be utilized to develop mapping population to map genomic regions conferring the resistance to downy mildew in cucumber.

Resequencing of 296 cultivated and wild lotus accessions unravels its evolution and breeding history.

Lotus (family: Nelumbonaceae) are perennial aquatic plants that represent one of the most ancient basal dicots. In the present study, we resequenced 296 lotus accessions from various geographical locations and germplasms to explore their genomic diversity and population structure. This germplasm set consisted of four accessions of American wild lotus and 292 accessions of Asian lotus, which were divided into four subgroups: wild, rhizome, flower and seed. Total single nucleotide polymorphisms (SNPs) suggested that the wild lotus had the highest variant number (7191010). Population structure and genome diversity analysis indicated that the American wild lotus demonstrated a distant genetic relationship with the Asian lotus. Furthermore, the seed and rhizome lotus groups had not originated from a single source but rather had a more complex multisource origin. Besides that, the seed lotus showed higher genetic diversity, which might have been due to the gene flow from the flower lotus to seed lotus by artificial crossing, and the rhizome lotus showed a much lower genetic diversity than the other groups. The present study provides SNP markers for lotus genomic diversity analysis, which will be useful for guiding lotus breeding.

Assessment of genetic diversity and population structure among a collection of Korean Perilla germplasms based on SSR markers.

Information on the genetic variation of genetic resource collections is very important for both the conservation and utilization of crop germplasms in genebanks. Var. frutescens of Perilla crop is extensively cultivated in South Korea as both an oil crop and a vegetable crop. We used SSR markers to evaluate the genetic diversity, genetic relationships, and population structure of 155 accessions of var. frutescens that have been selected as genetic resources for the development of leaf vegetable cultivars and preserved in the RDA-Genebank collection from South Korea. A total of 155 accessions of var. frutescens of Perilla crop collected in South Korea were obtained from the RDA-Genebank of the Republic of Korea. We selected 20 SSR markers representing the polymorphism of and adequately amplifying all the Perilla accessions. The average GD and PIC values were 0.642 and 0.592, respectively, with ranges of 0.244-0.935 and 0.232- 0.931. The genetic variability in the southern region of South Korea was higher than that in the central region. The clustering patterns were not clearly distinguished between the accessions of var. frutescens from the central and southern regions of South Korea. These results regarding the genetic diversity and population structure of the 155 accessions of var. frutescens of South Korea provide useful information for understanding the genetic variability of this crop and selecting and managing core germplasm sets in the RDA-Genebank of the Republic of Korea.

QRgls1.06, a major QTL conferring resistance to gray leaf spot disease in maize

Gray leaf spot (GLS) caused by Cercospora zeae-maydis and C. zeina is an extremely devastating leaf disease that limits maize production annually. The use of GLS-resistant maize hybrids is the most cost-effective approach for reducing losses. Resistance to GLS is quantitatively inherited in maize (Zea mays L.) and further sources of resistance remain to be analyzed. Here, we detected qRgls1.06, a major quantitative trait locus for GLS resistance in bin 1.06 that explained approximately 55% of the phenotype variance. Fine mapping over 2 consecutive years localized qRgls1.06 to a 2.38-Mb region. Homozygous qRgls1.06WGR/WGR plants in DZ01 background displayed higher GLS resistance and 100-grain weight than DZ01 plants. The GLS responses of several susceptible elite inbred lines were improved by the introduction of qRgls1.06 by marker-assisted backcrossing. Our findings extend the understanding of the genetic basis of resistance to GLS and provide a set of resistant germplasm for genetic improvement of resistance to GLS in maize.

The Role of Genetic Resources in Breeding for Climate Change: The Case of Public Breeding Programmes in Eighteen Developing Countries.

The role of plant breeding in adapting crops to climate changes that affect food production in developing countries is recognized as extremely important and urgent, alongside other agronomic, socio-economic and policy adaptation pathways. To enhance plant breeders’ capacity to respond to climate challenges, it is acknowledged that they need to be able to access and use as much genetic diversity as they can get. Through an analysis of data from a global survey, we explore if and how public breeders in selected developing countries are responding to climate challenges through a renewed or innovative use of plant genetic resources, particularly in terms of types of material incorporated into their breeding work as well as sources of such germplasm. It also looks at the possible limitations breeders encounter in their efforts towards exploring diversity for adaptation. Breeders are clearly considering climate challenges. In general, their efforts are aimed at intensifying their breeding work on traits that they were already working on before climate change was so widely discussed. Similarly, the kinds of germplasm they use, and the sources from which they obtain it, do not appear to have changed significantly over the course of recent years. The main challenges breeders faced in accessing germplasm were linked to administrative/legal factors, particularly related to obtaining genetic resources across national borders. They also underscore technical challenges such as a lack of appropriate technologies to exploit germplasm sets such as crop wild relatives and landraces. Addressing these limitations will be crucial to fully enhance the role of public sector breeders in helping to adapt vulnerable agricultural systems to the challenges of climate change.

Exploration and selection of elite Sd1 alleles for rice design breeding

Plant height is the important determinant for the yield formation of rice, and selecting of an optimal plant height is necessary during rice breeding to achieve ideal biomass and lodging resistance. In this study, allele variation of Sd1, the well-known “green revolution” gene, was clarified as the major factor for plant height segregation in the breeding populations from an indica and japonica cross. Two null sd1 alleles (sd1N1, sd1N2) and two functional Sd1 alleles (Sd1Jap and Sd1Ind) were characterized by newly developed functional markers, which demonstrated high efficiency for genotyping a large set of germplasms. We found that the null alleles, which were enriched in the modern indica but not japonica varieties in China, presented universal effects to shorten plant height despite the genetic backgrounds and environments. The effect of the Sd1Jap allele for plant height was weaker than that of Sd1Ind but sensitive to the genetic background of different subspecies, suggesting complex epistatic interactions between Sd1Jap and other plant height loci. In addition, Sd1Jap was identified to be compatible with some hybrid varieties recently developed in China, raising its potential value for hybrid rice breeding. Finally, we carried out a breeding practice by introgressing the null sd1 allele into the elite japonica variety Daohuaxiang, which suffers from severe lodging, and clarified the agronomic performance of the improved semi-dwarf line. This study will pave the way for the effective application of different Sd1 alleles in both inbred and hybrid breeding in the future.

Identification and validation of genetic loci for tiller angle in bread wheat.

Two major QTL for tiller angle were identified on chromosomes 1AL and 5DL, and TaTAC-D1might be the candidate gene for QTA.caas-5DL. An ideal plant architecture is important for achieving high grain yield in crops. Tiller angle (TA) is an important factor influencing yield. In the present study, 266 recombinant inbred lines (RILs) derived from a cross between Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895) was used to map TA by extreme pool-genotyping and inclusive composite interval mapping (ICIM). Two quantitative trait loci (QTL) on chromosomes 1AL and 5DL were identified with reduced tiller angle alleles contributed by ZM895. QTA.caas-1AL was detected in six environments, explaining 5.4-11.2% of the phenotypic variances. The major stable QTL, QTA.caas-5DL, was identified in all eight environments, accounting for 13.8-24.8% of the phenotypic variances. The two QTL were further validated using BC1F4 populations derived from backcrosses ZM871/ZM895//ZM871 (121 lines) and ZM871/ZM895//ZM895 (175 lines). Gene TraesCS5D02G322600, located in the 5DL QTL and designated TaTAC-D1, had a SNP in the third exon with 'A' and 'G' in ZM871 and ZM895, respectively, resulting in a Thr169Ala amino acid change. A KASP marker based on this SNP was validated in two sets of germplasm, providing further evidence for the significant effects of TaTAC-D1 on TA. Thus extreme pool-genotyping can be employed to detect QTL for plant architecture traits and KASP markers tightly linked with the QTL can be used in wheat breeding programs targeting improved plant architecture.

Genetic variation in the photosynthetic induction response in rice (Oryza sativa L.)

ABSTRACT Crop leaves growing under field conditions experience fluctuating light intensities. The photosynthetic response to a sudden increase in light intensity, which is termed the photosynthetic induction response, can potentially affect crop productivity. In the present study, the genetic variation in the photosynthetic induction response and the related gas exchange parameters in the rice diversity research set of germplasm (RDRS) were evaluated using two reference genotypes: Koshihikari and Takanari. Takanari is known to show superior induction response than Koshihikari. The photosynthetic induction response was found to be highly diverse in 59 rice genotypes. The cumulative CO2 fixation during the first 10 minutes after a transition from low to high light intensity (CCF10) differed by a factor of four between genotypes. The variation of CCF10 showed no relationship with light saturated photosynthetic rate (R = 0.21), but was significantly correlated with photosynthetic rate (A) under low light conditions (R = 0.88). Several genotypes showed even more rapid induction responses than that of Takanari. In particular, A of ARC 11094 and Rexmont both increased rapidly during the first two minutes of the induction response. The CCF10 of these two genotypes was approximately four times greater than that of Koshihikari. The rapid induction responses of Rexmont and ARC 11094 most likely resulted from the activation of CO2 fixation in mesophyll cells and CO2 diffusion from the air to the leaves, respectively. This study demonstrates that there is a large genetic variation in and, therefore, much potential for genetic improvement of, the photosynthetic induction response in rice.

Molecular characterization of popular rice (Oryza sativa L.) varieties of India and association analysis for blast resistance

Blast is a major biotic factor accountable for near-complete yield loss in rice (Oryza sativa L.). Thirty-seven leaf blast resistant lines were found out of 103 rice germplasm through phenotyping. Subsequent genotyping of the germplasm for five important blast resistance genes of India namely, Pitp, Pi1, Pi2, Pi9, and Pi54 using gene-specific markers revealed the prevalence of Pitp as more and Pi2 as least in the tested lines. An initial genetic diversity study showed the highest PIC value of 0.77 for RM234 defining its high polymorphic behaviour. Model-based and distance-based approaches showed a high correlation in displaying genetic diversity. The model-based structural analysis based on log-likelihood (∆k) displayed three clusters and remaining accessions under admixture. Distance-based analysis using Unweighted Pair Group Method with Arithmetic Mean method also divided the accessions into three major clusters. Analysis of molecular variance revealed a variation of 19% among the populations, while 81% within the populations. The association analysis using 101 SSR markers revealed ten newly identified marker-trait associations by General Linear Model and two marker-trait associations using Mixed Linear Model approach. These markers can be validated in a large set of germplasm and can be used in marker-assisted selection. The identified resistant sources having known genes can be readily used in the breeding programmes.

Resistance of the SoyNAM Parents to Seed and Root Rot Caused by Four Pythium Species

Some Pythium spp. cause damping off and root rot in soybeans and other crop species. One of the most effective management tools to reduce disease is host resistance; however, little is known about resistance in soybean to Pythium spp. The soybean nested associated mapping (SoyNAM) parent lines are a set of germplasms that were crossed to a single hub parent to create recombinant inbred line populations for the purpose of mapping agronomic traits. The SoyNAM parents were screened for resistance to Pythium lutarium, Pythium oopapillum, Pythium sylvaticum, and Pythium torulosum in separate assays to evaluate seed and root rot severity. Of the 40 SoyNAM parents, only 'Maverick' was resistant to the four species tested; however, 13 were resistant to three species. Other lines were resistant to two, one, or none of the species tested. Correlations between seed and root rot severity for the lines assessed were weak or insignificant. Results indicate that mechanisms of resistance to seed and root rot caused by Pythium spp. may not necessarily be the same.