Hybrid Genotypes Research Articles

Preserving tororaro’s legacy: conservation genetics of in-situ and ex-situ populations of Muehlenbeckia astonii (Polygonaceae)

ABSTRACT Tororaro, a Threatened Nationally Endangered species in eastern South Island and southern North Island, New Zealand, is primarily found in coastal or lowland droughty habitats with small, isolated populations, notably the largest on Kaitōrete Spit, Canterbury. Due to recent issues with the conservation management of the Kaitōrete Spit population, the importance of protecting this species has been highlighted. While widely cultivated in gardens for its horticultural appeal and resilience, recruitment failure in wild populations and the genetic structure and variation within wild and cultivated populations is unknown, which raises questions about in-situ and ex-situ conservation strategies. Microsatellite markers were developed to assess the level of natural variation present in wild populations and that of cultivated material present throughout New Zealand. The results reveal natural populations can be grouped into three clusters with a low to medium level of diversity for each cluster (Na = 1.647–3.647, Ho = 0.194–0.457, He = 0.181–0.478), and the diversity of each group is captured in cultivation (Na = 2.471–3.588, Ho = 0.207–0.511, He = 0.173–0.519). Cultivated material largely follows ecosourcing guidelines whereby cultivated plants in Wellington, Marlborough and Canterbury are often sourced from the regional meta-population, however, there are some exceptions that have implications for management of this species. In Otago, where M. astonii does not naturally occur, cultivated populations comprise representatives of all regional populations. An interesting outcome is that we recovered from among the cultivated plants several individuals that are likely to be putative intraspecific hybrids between plants from Wellington populations and those from either Marlborough or Canterbury; these hybrid genotypes are unknown in wild populations. Clonal plants were also represented among the wild and cultivated populations by individual plants having identical genotypes. We also demonstrate the utility of these markers across other Muehlenbeckia species.

Clinical Validation of a Prenatal Cell-Free DNA Screening Test for Fetal RHD in a Large U.S. Cohort.

To present a large U.S. clinical validation of a next-generation sequencing-based, noninvasive prenatal cell-free DNA test for fetal RHD. This clinical validation study assessed the performance of a commercially available, next-generation sequencing-based cell-free DNA test for fetal RHD status. Samples that passed quality metrics were included if the patient had a previously reported cell-free DNA result for fetal aneuploidy, maternal RhD-negative serology, newborn RhD serology, and maternal RHD deletion or RHD-CE-D hybrid(r's) genotype. Dizygotic twin pregnancies were excluded. Maternal and fetal RHD genotypes were evaluated with prospective cell-free DNA next-generation sequencing analysis. At the time of analysis, investigators were blinded to fetal RhD status. The cohort consisted of 655 pregnant patients with serologic results for RhD antigen. Patient demographics included a representative distribution of race and ethnicities in the RhD-negative U.S. population (74.0% White, 13.7% Hispanic, 7.0% Black, and 2.1% Asian). Cell-free DNA fetal RHD was not reported in two cases. There were zero false-negative cases; 356 of 356 fetuses were correctly identified as fetal RhD positive (sensitivity 100%, 95% CI, 98.9-100%). Of the 297 RhD-negative fetuses, 295 were correctly identified as RhD negative (specificity 99.3%, 95% CI, 97.6-99.8%). Of the fetuses with a negative RhD phenotype, the cell-free DNA test accurately identified three with the fetal RHD pseudogene (RHDΨ) genotype. Validation of this test in this large U.S. cohort of RhD-negative patients provides data on early and accurate noninvasive prenatal identification of fetal RHD genotype at 9 weeks of gestation or more. This test has the potential to assist patients and clinicians in the prevention and management of RhD alloimmunization.

Breeding of new kiwifruit (Actinidia chinensis) cultivars with yellow (golden) fleshed and superior characteristics

The most widely cultivated species globally is Actinidia deliciosa cv. ‘Hayward’. However, in recent years, consumers have shown greater demand for new varieties with novel flesh colour, flavour and appearance in international markets. To meet these expectations, one breeding study was started in 2016 at the University of Guilan in Iran to develop new kiwifruit cultivars with superior characteristics. In this breeding program, 201 female and 534 male hybrid genotypes were obtained from combinations of six different parents using the controlled cross-breeding technique. The evaluations were carried out over three consecutive stages. In the first stage, 201 female hybrid genotypes and control (‘Golden’) were evaluated based on 25 phenological and pomological traits. In the second stage, hybrids passed the desired threshold values in 7 key attributes were selected. Sensory testing in the next stage evaluated these selected hybrid genotypes more. As a result of the first stage, 30 hybrid genotypes with fruit weight (90 ≥ g) were selected. Then, in the second stage, 21 hybrids that showed acceptable dry matter, hue angle, flesh firmness, soluble solid content, acidity, and ascorbic acid were selected. Finally, 13 hybrid genotypes received high scores in sensory testing, and just two hybrid genotypes represented a 100% of novelty with positive texture. These genotypes were selected as potential cultivar candidates. In future studies, fruit yield, disease/pest resistance, and post-harvest performance trials of the 13 selected candidates will be evaluated at different sites. Thus, the ones that give the best results will be introduced to kiwifruit growers.

Genotypic Variation and Potential Mechanisms of Resistance against Multiple Insect Herbivores in Cranberries.

Plant genotypes often exhibit varying resistance levels to herbivores. However, the impact of this genotypic variation on resistance against multiple herbivores remains poorly understood, especially in crops undergoing recent process of domestication. To address this gap, we studied the magnitude and mechanism of resistance in 12 cranberry (Vaccinium macrocarpon) genotypes to three leaf-chewing herbivores - Sparganothis fruitworm (Sparganothis sulfureana), spotted fireworm (Choristoneura parallela), and spongy moth (Lymantria dispar) - along a domestication gradient (native 'wild' genotypes, 'early hybrid' genotypes, and 'modern hybrid' genotypes). Like cranberries, S. sulfureana and C. parallela are native to the United Sates, while L. dispar is an invasive pest. We measured the survival and growth of larvae on each genotype, as well as variation in plant performance (height and biomass) and leaf defensive chemical traits (C/N ratio, total phenolics, total proanthocyanidins, and flavonols levels) in these genotypes to elucidate potential resistance mechanisms. We found differences in C. parallela and L. dispar larval performance across genotypes, with larvae performing better on the modern hybrid genotypes, while S. sulfureana showed no differences. Morphological and chemical traits varied among genotypes, with total phenolics being the only trait correlated with C. parallela and L. dispar larval performance. Notably, the wild genotypes 'McFarlin' and 'Potter' had higher total phenolics and were more resistant to both herbivores than the modern hybrids 'Demoranville' and 'Mullica Queen.' This research contributes to a comprehensive understanding of the impact of crop domestication on multiple insect herbivores, offering insights for future breeding efforts to enhance host-plant resistance against agricultural pests.

Creation of true interspecies hybrids: Rescue of hybrid class with hybrid cytoplasm affecting growth and metabolism.

Interspecies hybrids have nuclear contributions from two species but oocyte cytoplasm from only one. Species discordance may lead to altered nuclear reprogramming of the foreign paternal genome. We reasoned that initial reprogramming in same species cytoplasm plus creation of hybrids with zygote cytoplasm from both species, which we describe here, might enhance nuclear reprogramming and promote hybrid development. We report in Mus species that (i) mammalian nuclear/cytoplasmic hybrids can be created, (ii) they allow development and viability of a previously missing and uncharacterized hybrid class, (iii) different oocyte cytoplasm environments lead to different phenotypes of same nuclear hybrid genotype, and (iv) the novel hybrids exhibit sex ratio distortion with the absence of female progeny and represent a mammalian exception to Haldane's rule. Our results emphasize that interspecies hybrid phenotypes are not only the result of nuclear gene epistatic interactions but also cytonuclear interactions and that the latter have major impacts on fetal and placental growth and development.

Identification of stable restorers and high-yielding hybrids using diverse sorghum male sterile cytoplasmic sources and established pollen parents under different water regimes

Sorghum hybrids demonstrated increased productivity and helped offset the decreasing cultivated areas, particularly in Asia. The diversity in cytoplasmic male sterility systems, stability of restorers and high yield of sorghum is an important factor for achieving food security and sustainability. In sorghum, hybrid production has been limited to A1 cytoplasmic source to date, primarily due to limited number of restorers on other cytoplasmic sources. This work aimed at filling this gap through diversifying and assessing the producibility and stability of cytoplasmic backgrounds across environments, evaluating the stability of restorers across cytoplasms and environments, and evaluating the performance of the hybrid F1 products under different water regimes across cropping seasons. The effects of genotypes and interactions between the genotypes and the tested environments were shown visually using GGE biplot, which also categorized the genotypes based on performance per se and stability. Analysis of variance revealed significant (P < 0.001) differences between genotypes, environments and their interaction components for all the plant characteristics studied. The various GGE biplot patterns revealed that the restorers G4 (IS 33844-5), G5 (M 35-1-19), G8 (ICSV 15014), and G10 (ICSR 13009) were stable across environments and cytoplasms. We observed the following order of superiority in cytoplasmic restoration and seed producibility, A2 >A1>A3 >A4. The A2 cytoplasm can therefore reliably offer seed producibility advantage to commercial seed producers. Furthermore, the which-won–where model for hybrid grain yield revealed specific adaptations of hybrid genotypes G143, G195 and G215 to first mega environment (E1 and E3), whereas G167, G110, and G112 were adapted to the second mega-environment (E2 and E4). With a GGE biplot goodness of fit of 70 % the best possible yield- and stability-based ranking of hybrid genotypes was G143, G215, G189, G200, G69, G162, G119, G54, and G81. The newly uncovered hybrid products should therefore be considered for downstream testing stages and candidates for release and commercial cultivation. Clearly, this work resulted in novel findings particularly in terms of seed producibility, universal restorers across the 4 cytoplasms and environments, and superior and stable hybrid products, all of which are expected to add value to conventional and heterosis breeding in the process of sorghum cultivar development.

Differential photosynthetic yield across a wide range of temperatures for Northern and invasive Watermilfoils

Eurasian watermilfoil (Myriophyllum spicatum) is one of the most challenging invasive aquatic plant species in Minnesota. Eurasian watermilfoil has hybridized with the native Northern watermilfoil (Myriophyllum sibiricum), creating a more complex issue when it comes to invasions. The hybridization of watermilfoil has increased difficulty for management and an underlying biological mechanism explaining this difficulty has yet to be determined. We compared the photosynthetic temperature response of the parental Northern and Eurasian parental genotypes to five hybrid watermilfoils using pulse amplitude modulated (PAM) chlorophyll fluorometry to determine if there are intrinsic physiological differences in photosynthesis between genotypes. We examined both the ratio of variable to maximal fluorescence (Fv/Fm) and light-adapted quantum yield of photosystem II (PSII) electron transfer (ΦPSII) every 5 °C from 0 to 45 °C representing sub- to supraoptimal water temperatures. On average, hybrids had 6% and 8% higher Fv/Fm and ΦPSII values respectively, than parental genotypes across all temperatures. In both parental and hybrid genotypes Fv/Fm values were consistent from 0 to 35 °C and declined 36% as water temperature approached 45 °C. Optimal water temperature for ΦPSII was between 25-35 °C and hybrids had 17% higher values for suboptimal temperatures between 5-15 °C. Our findings indicate that although the many strains of watermilfoil are morphologically similar, they differ in their photosynthetic capacity and may indicate heterosis. Innate differences between parental strains and hybrids could impact overall primary productivity, life history characteristics, and overall invasiveness. These factors could also be contributing to the documented management failures seen in field populations.

An efficient and easy-to-use protocol for induction of haploids in cucumber through parthenogenic embryo development

BackgroundCucumber (Cucumis sativus L.) is a model crop to study cell biology, including the development of haploids and doubled haploids in vegetable crops. In plant breeding, haploid and doubled haploids are valuable tools for developing pure homozygous inbred lines and accelerating genetic progress by reducing the time required for breeding cycles. Besides, the haploids are also valuable in genomic studies. We are reporting the induction of haploids in cucumber involving gynoecious and parthenocarpic genotypes for the first time. This study aimed to assess the efficient induction of haploids through pollination with gamma-irradiated pollen in cucumber. The effect of gamma irradiation dose on pollen viability and germination, fruit setting percentage, seed development, and haploid embryo development in cucumber hybrid genotypes were studied in detail. The goal was to utilize this information to produce haploid plants for genomics and transformation works in this model vegetable crop.ResultsPollination was done on six cucumber genotypes using varying doses of gamma rays (100, 200, 300, 400, and 500 Gy). Genotypes, doses of irradiation, and embryo developmental stage influenced the successful generation of in-vitro haploid plants. The optimal timeframe for embryo rescue was found to be 25 to 30 days after pollination. Haploid embryos were effectively induced using irradiated pollen at 400 to 500 Gy doses. Parthenogenetic plantlets were analyzed, and their ploidy level was confirmed through stomatal physiology, cytology (mitosis), and flow cytometry methods.ConclusionThrough parthenogenic embryo development, it is possible to induce a large number of haploids in cucumber. This technique’s power lies in its ability to streamline the breeding process, enhance genetic gain, and produce superior cultivars that contribute to sustainable agriculture and food security.

Performance evaluation of hybrid maize (Zea mays L.) in Burkina Faso, sub-Saharan region of Africa

Maize (Zea mays L.) is a staple food for many people in Burkina Faso. The cultivation of maize hybrid genotypes plays a crucial role in increasing maize production and productivity. Feeding the growing population of the country, expected to reach thirty million by 2035, using hybrid genotypes of maize is a challenge. The objective of this study was to identify the hybrid maize genotypes having a best adaptability in the agro-ecological context of Burkina Faso. Nine (09) hybrid maize genotypes were evaluated during the 2018/2019 cropping season, in nine locations of the country characterized by a rainfall varying between 800 and 1200 mm. The experimental design was a Randomized Complete Block Design (RCBD) with three replications. The results showed that grain yield of the hybrids varied depending on the genotype nature and the cropping environment. The use of hybrid maize significantly increased the grain yield per hectare in maize production. Among the tested hybrid maize genotypes, SD1 (9.054 tons ha−1), SD3 (7.683 tons ha−1), and SD6 (9.385 tons ha−1) significantly presented higher yields. Based on the grain yield, the best growing environments of hybrid maize are NEBOUM1, BAMA and SOUNGALODAGO. The best genotypes for most of the environments are the hybrids of pure line varieties. The heritability was more than 80 % for all the studied yield traits.

Genotypic Selection Using Quantitative Trait Loci for Better Productivity under High Temperature Stress in Tomato (Solanum lycopersicum L.)

High temperature stress affects tomato production both in tropical and sub-tropical environments worldwide. To explore genetic variation for heat tolerance in tomato, 329 transcontinental tomato genotypes were evaluated at the Ministry of Municipality and Environment (MME) greenhouses near Doha, Qatar, where the average daytime temperature was 38 °C with a big fluctuation during the tomato growth season. A preliminary phenotypic analysis identified a panel of 71 hybrid and pure-line tomato genotypes for more detailed studies. The selected subset was examined in the greenhouse using a randomized complete block design under heat stress. The materials were phenotyped for fruit size, fruit weight, fruit hardness, fruit locules, fruit set, total soluble solids (TSS), and fruit yield. Significant phenotypic differences among genotypes were observed for all the traits assessed. To explore the genetic basis of the variation among the examined genotypes, the subset was genotyped using 104 SNP markers identified in previous heat-tolerance genome-wide association studies (GWAS). Nineteen QTL-associated SNP markers could reliably select heat-tolerant genotypes in terms of better fruit yield, fruit set, and TSS. These markers are located on chromosome 1, 5, 6, 8, 9, and 12. Interestingly, two clusters of markers on chromosome 6 were linked to significant effects on yield, fruit set, and TSS under high temperature. Eighteen out of nineteen SNP markers were mapped within a gene body. Based on the phenotypic and the genotypic analysis, an elite set of five genotypes was selected for approval for heat stress environments in Qatar. The aim of the present work is to provide significant results that are exploitable not only in the Qatar region but also worldwide. Specifically, the 19 molecular markers identified in this study can serve as useful tools for breeders in selecting heat-tolerant material.

Phenotypic Evaluation of Saccharum spp. Genotypes during the Plant-Cane Crop for Biomass Production in Northcentral Mississippi

Saccharum is relatively new to 33° N latitude. S. spontaneum readily hybridizes with commercial sugarcane (Saccharum spp.) and lends cold tolerance and greater yield to the hybrid progeny, called energycane. Since 2007, there have been numerous new hybrid and backcross energycane genotypes developed but there is a paucity of information about them. Twenty energycane genotypes were tested in the first season of growth from cane propagules (plant cane; PC) against Ho 02-113 (a control) for two site-years in northcentral Mississippi. Grand (exponential) growth continued into October. The prevailing paradigm is that tonnage is what matters. Except for percentage cellulose, all factors tested (dry matter yield, extractable juice volume, °Brix, theoretical ethanol from fermentation, theoretical ethanol from cellulose, and total theoretical ethanol) were greater from the second site-location compared to the first. Dry matter yield (DMY) and total theoretical ethanol yield (TTEY) were moderately correlated. Over the two years of this test only Ho 14-9213 exceeded in mean DMY of Ho 02-113. Sixteen of the 19 test genotypes in this test equaled or exceeded the mean TTEY of Ho 02-113.

Origins of Susceptibility to Insect Herbivores in High-Yielding Hybrid and Inbred Rice Genotypes.

Several studies have reported higher damage from insect herbivores to hybrid compared to inbred (pure line) rice. We used a collection of 20 hybrid and 12 inbred genotypes from diverse origins to test the hypotheses that hybrid rice susceptibility is due to (a) the hybrid plant type and/or (b) rice phylogeny. We challenged the genotypes with Nilaparvata lugans (BPH), Sogatella furcifera (WBPH) and Scirpophaga incertulas (YSB) in greenhouse and screenhouse bioassays and monitored herbivores in field plots. We used single nucleotide polymorphic (SNP) markers to assess genetic similarities between the genotypes and found that the hybrids and inbreds formed two distinct clusters regardless of origin. In the screenhouse, hybrids were more susceptible than inbreds to YSB; however, resistant hybrids and susceptible inbreds were also apparent from both the screenhouse and field plots. Plant biomass was the best predictor of susceptibility to YSB. Plant origin had a greater effect than plant type on susceptibility to BPH and WBPH. WBPH was the most abundant planthopper in the field plots where numbers were highly correlated with planthopper fitness in the greenhouse bioassays. Our results provide evidence that high-yielding hybrids that are relatively resistant to herbivores can be achieved through careful breeding. The avoidance of susceptible genotypes during breeding should remain a key element of integrated rice pest management.

Vitis species for stress tolerance/resistance

AbstractMany wild plant species are actually true treasures of our world. The value of these treasures is better understood today and many wild species are used for different purposes. Also Vitis species are among the most important species with their ancient history. China and North America are the native ranges of many Vitis species that survive to the present day, most of which have survived by natural selection. These species have attracted the attention of plant breeders for many years due to their resistance to various biotic and abiotic stress conditions, and they have used these species to develop new cultivars. In parallel with the developments in the field of biotechnology, interspecific hybrid genotypes obtained in breeding research for resistance to different stress conditions can be obtained in accordance with the targets in a much shorter time. In these investigations, gene regions in Vitis species with resistance genes were transferred to new hybrid genotypes. Additionally, these species have been used as parents in many breeding programs in different countries due to their resistance to biotic stress conditions, especially fungal diseases. Similar breeding research has been carried out on tolerance to abiotic stress conditions, and interspecific cross-breeding have been made to develop hybrid genotypes that are more tolerant to many abiotic stress conditions. In recent years, resistance and high-quality wine and table grape cultivars obtained from rossbreeding have begun to be used in production. As a result, newly developed interspecific hybrid grapes can be grown with much lower production costs in accordance with the sustainable viticulture model.

Low Light at Specific Growth Stage Affects Photoassimilates Transportation, Seed Quality and Yield in Brassica napus L.

ABSTRACTIn many parts of the world, solar radiation has decreased during the past 50 years due to industrialisation‐induced elevations in air aerosols which has negatively impacted crop productivity. Climate change threatens rapeseed (Brassica napus L.) production due to shade stress caused by reduced light radiation. However, studies on how shade affects photosynthetic mechanisms in rapeseed (leaves and pod wall) are not well documented. Understanding the mechanisms of shade on yield formation in rapeseed is important for breeding shade‐tolerant rapeseed varieties and optimising agricultural management practices in low‐light areas. Therefore, this study assesses the impacts of ‘global dimming’ simulated by shading at a specific period on rapeseed's photosynthetic behaviour, yield and seed quality. A two‐factor split‐plot design was arranged with three shading treatments (CK, FS and PS) and two hybrid genotypes (Chuannong and Zhongyouza) of rapeseed. We observed that shading at the flowering stage (FS) significantly inhibited the leaf area index, chlorophyll content, photosynthetic efficiency and enzymatic activities of both genotypes. Besides that, shading at pod development stage (PS) substantially declined the pod photosynthetic characteristics and transportation of carbohydrates towards economic organ (seeds) which directly decreased the yield of rapeseed. We found that PS treatment remarkably declined the oil content of both genotypes. According to the results, the photosynthetic capacity of rapeseed pod wall had a greater impact on yield and seed quality than leaves. Therefore, improving the photosynthetic capacity and material transport efficiency of the pod wall is a potential measure to increase the yield of rapeseed under shade stress. This study provides a new insight into the effects of shade on rapeseed production and provides a valuable reference for rapeseed breeding techniques to develop high‐yielding genotypes by enhancing the photosynthetic efficiency of rapeseed pod wall in low‐light conditions.

GIS-based G × E modeling of maize hybrids through enviromic markers engineering.

Through enviromics, precision breeding leverages innovative geotechnologies to customize crop varieties to specific environments, potentially improving both crop yield and genetic selection gains. In Brazil's four southernmost states, data from 183 distinct geographic field trials (also accounting for 2017-2021) covered information on 164 genotypes: 79 phenotyped maize hybrid genotypes for grain yield and their 85 nonphenotyped parents. Additionally, 1342 envirotypic covariates from weather, soil, sensor-based, and satellite sources were collected to engineer 10 K synthetic enviromic markers via machine learning. Soil, radiation light, and surface temperature variations remarkably affect differential genotype yield, hinting at ecophysiological adjustments including evapotranspiration and photosynthesis. The enviromic ensemble-based random regression model showcases superior predictive performance and efficiency compared to the baseline and kernel models, matching the best genotypes to specific geographic coordinates. Clustering analysis has identified regions that minimize genotype-environment (G × E) interactions. These findings underscore the potential of enviromics in crafting specific parental combinations to breed new, higher-yielding hybrid crops. The adequate use of envirotypic information can enhance the precision and efficiency of maize breeding by providing important inputs about the environmental factors that affect the average crop performance. Generating enviromic markers associated with grain yield can enable a better selection of hybrids for specific environments.

Root-Zone Bacterial Diversity in Field-Grown Individual Plants from Alfalfa Lines with Wild Relatives in Their Genetic Backgrounds

Alfalfa (Medicago sativa L.) is a vitally important perennial fodder legume worldwide. Given their particular traits, alfalfa crop wild relatives (CWRs) could be used to develop cultivars that can tolerate extreme environmental and climatic conditions. Until now, researchers have overlooked the composition and structure of bacterial communities in the root zone of alfalfa and its relevant CWRs and their influence on forage performance under actual field conditions. In this study, high-throughput sequencing of 16S rRNA analysis was performed to investigate the diversity and assemblies of bacterial communities in the bulk soil and in the root zone of individual field-grown Medicago plants arranged in a honeycomb selection design. The plants used in this study were M. sativa × M. arborea hybrids (Genotypes 6 and 8), the closely-related M. sativa nothosubsp. varia (Martyn) Arcang. (Genotype 13), and M. sativa ssp. sativa (Genotype 20). The bacterial communities in the root-zone samples and the assemblies in the bulk soil differed significantly. Genotype 13 was found to have distinct bacterial assemblies from the other genotypes while exhibiting the lowest forage productivity. These findings suggest that plant productivity may influence the composition of bacterial communities in the root zone. Biomarker analysis conducted using linear discriminant analysis (LDA) revealed that only members of the Rhizobiales order were enriched in the M. sativa nothosubsp. varia root zone whereas taxa belonging to Sphingomonas and various Bacteriodota were enriched in the other genotypes. Of the shared taxa identified in the root zone of the Medicago lines, the abundance of specific taxa, namely, Flavisolibacter, Stenotrophomonas, and Sphingomonas, were positively associated with forage yield. This pioneering study, in which the root zones of individual Medicago plants under actual field conditions were examined, offers evidence of differences in the bacterial composition of alfalfa genotypes with varying genetic backgrounds. Its findings indicate that particular bacterial taxa may favorably influence plant performance. This study covered the first six months of crop establishment and paves the way for further investigations to advance understanding of how shifts in bacterial assemblies in alfalfa roots affect plant performance over time.

High resolution mapping of a novel non-transgressive hybrid susceptibility locus in barley exploited by P. teres f. maculata

Hybrid genotypes can provide significant yield gains over conventional inbred varieties due to heterosis or hybrid vigor. However, hybrids can also display unintended negative attributes or phenotypes such as extreme pathogen susceptibility. The necrotrophic pathogen Pyrenophora teres f. maculata (Ptm) causes spot form net blotch, which has caused significant yield losses to barley worldwide. Here, we report on a non-transgressive hybrid susceptibility locus in barley identified between the three parental lines CI5791, Tifang and Golden Promise that are resistant to Ptm isolate 13IM.3. However, F2 progeny from CI5791 × Tifang and CI5791 × Golden Promise crosses exhibited extreme susceptibility. The susceptible phenotype segregated in a ratio of 1 resistant:1 susceptible representing a genetic segregation ratio of 1 parental (res):2 heterozygous (sus):1 parental (res) suggesting a single hybrid susceptibility locus. Genetic mapping using a total of 715 CI5791 × Tifang F2 individuals (1430 recombinant gametes) and 149 targeted SNPs delimited the hybrid susceptibility locus designated Susceptibility to Pyrenophora teres 2 (Spt2) to an ~ 198 kb region on chromosome 5H of the Morex V3 reference assembly. This single locus was independently mapped with 83 CI5791 × Golden Promise F2 individuals (166 recombinant gametes) and 180 genome wide SNPs that colocalized to the same Spt2 locus. The CI5791 genome was sequenced using PacBio Continuous Long Read technology and comparative analysis between CI5791 and the publicly available Golden Promise genome assembly determined that the delimited region contained a single high confidence Spt2 candidate gene predicted to encode a pentatricopeptide repeat-containing protein.

Selection of Saccharum spp. × Saccharum spontaneum progeny for sugar and biomass traits

ABSTRACT This study evaluated an interspecific hybrid (Saccharum spp. × S. spontaneum) population with the aim of developing germplasm for use in both sugar and bioenergy (biomass) production. Specific objectives were to determine the genetic variability and heritability among the interspecific hybrid progenies for traits of economic importance and to use the Best Linear Unbiased Predictions (BLUPs) to determine their genotypic values. The 46 interspecific hybrids used in this study originated from crossing commercial sugarcane cultivars (UT5, F152, and KK07–559) as female and S. spontaneum clones (THS98–41, THS98–91, THS98–95, THS98–94, and THS97–51) as male parents. There were significant residual variances, attributed to the small plot size, but the juice quality traits were measured with relatively higher precision than other traits. Selection recommendations varied for different traits, suggesting selection pressure could be moderate to high for juice quality traits and moderate for yield-related traits. No hybrid genotypes were found to outperform cultivar parents for traits such as commercial cane sugar and low fiber, necessitating further germplasm enhancement for improvement of varieties destined for sugar production. On the contrary, transgressive segregation was observed for cane yield and other traits influencing biomass yield. The production potential of these hybrids could be tested in larger plots across multiple locations.

Genetic profile of RHCE, Kell, Duffy, Kidd, Diego and MNS hybrid glycophorins blood groups in ethnic northeastern Thais: Alleles, genotypes and risk of alloimmunisation.

Antibodies against blood group antigens play a key role in the pathophysiology of haemolytic transfusion reactions (HTRs) and haemolytic disease of the fetus and newborn (HDFN). This study aimed to determine the frequencies of alleles, genotypes, and risk of alloimmunisation of clinically significant blood group systems in ethnic northeastern Thais. In total, 345 unrelated, healthy, ethnic northeastern Thais were tested using the in-house PCR-sequence specific primers (PCR-SSP) method for simultaneously genotyping of RHCE, Kell, Duffy, Kidd, Diego and MNS glycophorin hybrids and results confirmed by Sanger sequencing. In this cohort, the alleles RHCE*C (81.0%) and RHCE*e (84.8%) were more prevalent than RHCE*c (19.0%) and RHCE*E (15.2%). The most common predicted haplotype combinations of the RHCE alleles were C+c-E-e+(R1R1) (59.4%) followed by the C+c+E+e+ (R1R2) (20.6%) and C+c+E-e+ (R1r) (11.3%). The KEL*01 allele was not found in this study. The frequencies of FY*01 and FY*02 were 88.3% and 11.7%, respectively. The genotype FY*02/02 was found in four samples (1.2%). The frequencies of JK*01 and JK*02 were 52.5% and 47.5%, respectively. Homozygous JK*02/02 was found in 81 samples (23.5%). The frequencies of DI*01 and DI*02 were 0.6% and 99.4%, respectively. In total, 64 samples (18.6%) were found to carry the MNS glycophorin hybrids. Our results indicated a possible high risk of c, E, Fyb, Jka, Jkb and Mia alloimmunisation in these populations. Moreover, methods established for genotyping clinically significant blood groups in this study can now be utilised in routine clinical application.

Genetic variation in Zea mays influences microbial nitrification and denitrification in conventional agroecosystems

Abstract Background and Aims Nitrogenous fertilizers provide a short-lived benefit to crops in agroecosystems, but stimulate nitrification and denitrification, processes that result in nitrate pollution, N2O production, and reduced soil fertility. Recent advances in plant microbiome science suggest that genetic variation in plants can modulate the composition and activity of rhizosphere N-cycling microorganisms. Here we attempted to determine whether genetic variation exists in Zea mays for the ability to influence the rhizosphere nitrifier and denitrifier microbiome under “real-world” conventional agricultural conditions. Methods To capture an extensive amount of genetic diversity within maize we grew and sampled the rhizosphere microbiome of a diversity panel of germplasm that included ex-PVP inbreds (Z. mays ssp. mays), ex-PVP hybrids (Z. mays ssp. mays), and teosinte (Z. mays ssp. mexicana and Z. mays ssp. parviglumis). From these samples, we characterized the microbiome, a suite of microbial genes involved in nitrification and denitrification and carried out N-cycling potential assays. Results Here we are showing that populations/genotypes of a single species can vary in their ecological interaction with denitrifers and nitrifers. Some hybrid and teosinte genotypes supported microbial communities with lower potential nitrification and potential denitrification activity in the rhizosphere, while inbred genotypes stimulated/did not inhibit these N-cycling activities. These potential differences translated to functional differences in N2O fluxes, with teosinte plots producing less GHG than maize plots. Conclusion Taken together, these results suggest that Zea genetic variation can lead to changes in N-cycling processes that result in N leaching and N2O production, and thereby are selectable targets for crop improvement. Understanding the underlying genetic variation contributing to belowground microbiome N-cycling into our conventional agricultural system could be useful for sustainability.