Inbred Lines Research Articles

Integrative multi-omic analysis identifies genes associated with cuticular wax biogenesis in adult maize leaves.

Studying the genetic basis of leaf wax composition and its correlation with leaf cuticular conductance (gc) is crucial for improving crop productivity. The leaf cuticle, which comprises a cutin matrix and various waxes, functions as an extracellular hydrophobic layer, protecting against water loss upon stomatal closure. To address the limited understanding of genes associated with the natural variation of adult leaf cuticular waxes and their connection to gc, we conducted statistical genetic analyses using leaf transcriptomic, metabolomic, and physiological data sets collected from a maize (Zea mays L.) panel of ∼300 inbred lines. Through a random forest analysis with 60 cuticular wax traits, it was shown that high molecular weight wax esters play an important role in predicting gc. Integrating results from genome-wide and transcriptome-wide studies (GWAS and TWAS) via a Fisher's combined test revealed 231 candidate genes detected by all three association tests. Among these, 11 genes exhibit known or predicted roles in cuticle-related processes. Throughout the genome, multiple hotspots consisting of GWAS signals for several traits from one or more wax classes were discovered, identifying four additional plausible candidate genes and providing insights into the genetic basis of correlated wax traits. Establishing a partially shared genetic architecture, we identified 35 genes for both gc and at least one wax trait, with four considered plausible candidates. Our study enhances the understanding of how adult leaf cuticle wax composition relates to gc and implicates both known and novel candidate genes as potential targets for optimizing productivity in maize.

Variation in rye (Secale cereale L.) inbred lines with different type of glaucousness

Variation in rye (Secale cereale L.) inbred lines with different type of glaucousness

Identification of genetic loci for powdery mildew resistance in common wheat.

Powdery mildew (PM) poses an extreme threat to wheat yields and quality. In this study, 262 recombinant inbred lines (RILs) of Doumai and Shi 4185 cross were used to map PM resistance genes across four environments. High-density genetic linkage map of the Doumai/Shi 4185 RIL population was constructed using the wheat Illumina iSelect 90K single-nucleotide polymorphism (SNP) array. In total, four stable quantitative trait loci (QTLs) for PM resistance, QPm.caas-2AS, QPm.caas-4AS, QPm.caas-4BL, and QPm.caas-6BS, were detected and explained 5.6%-15.6% of the phenotypic variances. Doumai contributed all the resistance alleles of QPm.caas-2AS, QPm.caas-4AS, QPm.caas-4BL, and QPm.caas-6BS. Among these, QPm.caas-4AS and QPm.caas-6BS overlapped with the previously reported loci, whereas QPm.caas-2AS and QPm.caas-4BL are potentially novel. In addition, six high-confidence genes encoding the NBS-LRR-like resistance protein, disease resistance protein family, and calcium/calmodulin-dependent serine/threonine-kinase were selected as the candidate genes for PM resistance. Three kompetitive allele-specific PCR (KASP) markers, Kasp_PMR_2AS for QPm.caas-2AS, Kasp_PMR_4BL for QPm.caas-4BL, and Kasp_PMR_6BS for QPm.caas-6BS, were developed, and their genetic effects were validated in a natural population including 100 cultivars. These findings will offer valuable QTLs and available KASP markers to enhance wheat marker-assisted breeding for PM resistance.

Co-localization of quantitative trait loci for pod and kernel traits and development of molecular marker for kernel weight on chromosome Arahy05 in peanut (Arachis hypogaea L.)

Key messageStable QTL for pod and kernel traits were co-localized on chromosome Arahy05, and an INDEL marker at 106,411,957 on Arahy05 was developed and validated to be useful for marker-assisted selection of kernel weight.Pod and kernel traits, such as hundred pod weight (HPW), and hundred kernel weight (HKW), along with pod and kernel sizes, are pivotal determinants of yield in peanut breeding programs. This study sought to identify quantitative trait loci (QTL) that are associated with these pod and kernel traits in peanuts. To achieve this, a recombinant inbred line (RIL) population, was derived from a cross between Yuhua15, a cultivar known for its high yield, and a germplasm accession W1202. The investigation uncovered stable and major QTL that are significantly associated with both pod and kernel weight and were consistently co-localized on chromosomes Arahy05 and Arahy08. Furthermore, an INDEL marker was identified and characterized in the QTL interval on Arahy05. An extensive re-sequencing analysis comprising 395 germplasm accessions led to the discovery of two principal haplotypes within a 500-kb window flanking the aforementioned INDEL marker. The haplotypes exhibited a significant correlation with the HKW in our diverse panel of germplasm accessions. Notably, the 170 accessions harboring the haplotype associated with an increased HKW primarily represented botanical varieties, specifically Arachis hypogaea var. hypogaea and A. hypogaea var. hirsuta. On the other hand, the 137 accessions associated with the alternative haplotype, which corresponded to a reduced HKW, were predominately identified as belonging to botanical varieties within A. hypogaea subsp. fastigiata. The INDEL marker located on Arahy05, which demonstrates close linkage to the pod and kernel traits, would be an efficient approach for marker-assisted selection (MAS) of pod and kernel weight in breeding programs.

Screening and Identification of Aluminium Toxicity Tolerant Lentil (Lens culinaris Medik.) RILs based on Root Growth Studies and Organic Acid Exudation under Hydroponics

Background: Aluminium (Al) stress is among the prime limitations of crop production including Lentil, in acidic soils as Al solubilizes into phytotoxic forms at low pH causing root growth inhibition, minimizing plant-vigor and yield. The current study was performed to identify the Al tolerant RILs based on root-regrowth studies, short term growth culture and organic acid exudation in reaction to Al toxicity under hydroponics. Methods: The study involved screening for Al toxicity tolerance in recombinant inbred lines (RILs) population of lentil through root re-growth studies, short term growth response method under hydroponics treated with toxic concentration of Al (148 µM), organic acid exudation using HPLC and correlation analysis among the traits. Result: ANOVA for root and shoot traits revealed presence of highly significant genotypic differences for all the traits. High GCV along with high H2bs and GA% were observed for the traits revealing the influence of additive genes and suggested reliable selection of these traits for Al toxicity tolerance. Citric acid was exudated in highest amount in all the genotypes and was positively and significantly correlated with RRG. Based on the hydroponics study and organic acid exudation, RILs identified as tolerant were LRIL-10, LRIL-37, LRIL-68, LRIL-96, LRIL-97, LRIL-113, LRIL-125, LRIL-133, LRIL-143, LRIL-144 and LRIL-148. With further evaluation, these RILs may serve as important Al toxicity tolerant varieties suitable for acidic soil conditions. Also, these lines may serve as donors of Al toxicity loci and mapping of Al tolerance genes.

Insights into the genetic divergence in Asiatic cotton (Gossypium arboreum L.) germplasm for fibre-quality traits

Abstract Asiatic cotton (Gossypium arboreum L.) has evolved in the Indian subcontinent and is known for its adaptability to low-input management conditions. In the present study, 300 diverse G. arboreum lines, including 100 Nandyal arboreum breeding lines (NAB), 132 Arboreum germplasm collections (AGC) and 68 long-linted arboreum genotypes (LLA), were evaluated for fibre quality to assess the diversity among them and to identify promising genotypes with desirable fibre traits. Significant variations were observed among the genotypes for the studied fibre-quality traits. Principal component analysis showed that the traits micronaire (Mic) and elongation percentage (E%) followed by upper half mean length (UHML) and bundle tenacity (tenacity) were the most significant contributors to variation. Cluster analysis based on the Euclidian distance method showed 16 clusters among 300 G. arboreum genotypes. The genotypes in cluster 4 have desirable UHML, tenacity and UI (uniformity index) traits, and cluster 12 has Mic and E% traits. Furthermore, the number of genotypes with desirable fibre-quality traits was found to be higher in the AGC group than in the LLA and NAB groups. The trait tenacity followed by the UHML showed relatively higher Shannon–Weiner diversity index values across different genotypic groups. Based on the superior performance, the genotypes PA 847, PA 809, PA 837, PA 863, NDLA 3147-2, NDLA 2974 and NDLA 3081 were found to be having desirable fibre traits. The identified promising genotypes are valuable genetic resources for improving fibre quality in G. arboreum cotton.

Elucidating the genetic potential of hybrids derived from elite maize (Zea mays L.) inbreds for economic traits under North-Western Himalayan condition

Abstract This study was conducted to evaluate the combining ability of newly acquired maize inbred lines over the environments. Twenty-eight crosses developed by crossing eight elite inbreds in a half-diallel mating design were evaluated during kharif, 2019 for 12 agro-morphological traits in RBD with two replications at two different environments reflecting diverse agro-climatic and ecological conditions of North-Western Himalayas (SAREC, Kangra and HAREC, Bajaura). Analysis of variance showed that there was sufficient amount of genetic variability in the material studied. In accordance to Bartlett’s test, error variance was homogeneous only for six traits. Estimates of σ2SCA were higher as compared to σ2GCA both within and across environments for all the traits, except days to 75 per cent brown husk at Kangra, representing prevalence of non-additive gene action for these traits. The inbred line B73 at Bajaura, and LM14 at Kangra were found to be good general combiner for most traits. The inbreds with good GCA can be used as potential parents for the development of high yielding single cross maize hybrids. The hybrid combinations namely, B73 × BAJIM1811 and BAJIM1522 × BAJIM1811 were identified as potentially superior ones at Kangra and Bajaura environments. The identified promising hybrids need further assessment for their superiority in performance across the locations and over years. Keywords: General combining ability, specific combining ability, gene action and maize.

Mining of Oil Content Genes in Recombinant Maize Inbred Lines with Introgression from Temperate and Tropical Germplasm.

The oil content of maize kernels is essential to determine its nutritional and economic value. A multiparent population (MPP) consisting of five recombinant inbred line (RIL) subpopulations was developed to elucidate the genetic basis of the total oil content (TOC) in maize. The MPP used the subtropical maize inbred lines CML312 and CML384, along with the tropical maize inbred lines CML395, YML46, and YML32 as the female parents, and Ye107 as the male parent. A genome-wide association study (GWAS) was performed using 429 RILs of the multiparent population across three environments, employing 584,847 high-quality single nucleotide polymorphisms (SNPs). Furthermore, linkage analysis was performed in the five subpopulations to identify quantitative trait loci (QTL) linked to TOC in maize. Through QTL mapping and GWAS, 18 QTLs and 60 SNPs that were significantly associated with TOC were identified. Two novel candidate genes, Zm00001d029550 and Zm00001d029551, related to TOC in maize and located on chromosome 1 were reported, which have not been previously reported. These genes are involved in biosynthesis, lipid signal transduction, plant development and metabolism, and stress responses, potentially influencing maize TOC. Haplotype analysis of Zm00001d029550 and Zm00001d029551 revealed that Hap3 could be considered a superior haplotype for increasing TOC in maize. A co-located SNP (SNP-75791466) on chromosome 1, located 5648 bp and 11,951 bp downstream of the candidate genes Zm00001d029550 and Zm00001d029551, respectively, was found to be expressed in various maize tissues. The highest expression was observed in embryos after pollination, indicating that embryos are the main tissue for oil accumulation in maize. This study provides a theoretical basis for understanding the genetic mechanisms underlying maize TOC and developing high-quality, high-oil maize varieties.

Accelerating genetic gain through strategic speed breeding in spring wheat

AbstractSpring wheat (Triticum aestivum L.) is a popular bread wheat with high milling and baking requirements. Vernalization is not required for spring wheat, which allows for fast growth under manipulated conditions. This experiment's objective was rapid development of inbred lines of hard red spring wheat throughout the off‐season and preserve enough genetic variability to perform selection. A total of 1575 F2 heads from three distinct populations were randomly harvested in the field‐season 2021. To break seed dormancy, seeds were held for 2 days at 0°C. Three breeding cycles were performed through single seed descent under manipulated growth condition during the off‐season 2021–2022. We were able to harvest plant materials as quickly as 54 days after planting in comparison to 110 days average field season. We lost a total of 36.4% during the three off‐season fast advancement generations and 711 genotypes reached the F5:6 generation with enough seed to perform a partially replicated small plot yield trial at two locations during the 2022 field‐season. Response traits collected included grain yield, grain protein, plant height, days to heading, and bacterial leaf streak (Xanthomonas transluens) disease severity. Heritability of collected traits varied between 0.61 and 0.92. Although we had considerable loss during the speed breeding, we were able to identify superior genotypes compared to the parents.

The marine environmental microbiome mediates physiological outcomes in host nematodes.

Nematodes are the most abundant metazoans in marine sediments, many of which are bacterivores; however, how habitat bacteria affect physiological outcomes in marine nematodes remains largely unknown. RESULTS: Here, we used a Litoditis marina inbred line to assess how native bacteria modulate host nematode physiology. We characterized seasonal dynamic bacterial compositions in L. marina habitats and examined the impacts of 448 habitat bacteria isolates on L. marina development, then focused on HQbiome with 73 native bacteria, of which we generated 72 whole genomes sequences. Unexpectedly, we found that the effects of marine native bacteria on the development of L. marina and its terrestrial relative Caenorhabditis elegans were significantly positively correlated. Next, we reconstructed bacterial metabolic networks and identified several bacterial metabolic pathways positively correlated with L. marina development (e.g., ubiquinol and heme b biosynthesis), while pyridoxal 5'-phosphate biosynthesis pathway was negatively associated. Through single metabolite supplementation, we verified CoQ10, heme b, acetyl-CoA, and acetaldehyde promoted L. marina development, while vitamin B6 attenuated growth. Notably, we found that only four development correlated metabolic pathways were shared between L. marina and C. elegans. Furthermore, we identified two bacterial metabolic pathways correlated with L. marina lifespan, while a distinct one in C. elegans. Strikingly, we found that glycerol supplementation significantly extended L. marina but not C. elegans longevity. Moreover, we comparatively demonstrated the distinct gut microbiota characteristics and their effects on L. marina and C. elegans physiology. Given that both bacteria and marine nematodes are dominant taxa in sedimentary ecosystems, the resource presented here will provide novel insights to identify mechanisms underpinning how habitat bacteria affect nematode biology in a more natural context. Our integrative approach will provide a microbe-nematodes framework for microbiome mediated effects on host animal fitness.

Molecular mechanisms of heterosis under drought stress in maize hybrids Zhengdan7137 and Zhengdan7153.

Maize is one of the most successful crops in utilizing heterosis which significantly improves maize stresses resistance and yield. Drought is a destructive abiotic stress that significantly reduces crop yield, particularly in maize. Drought stress and re-watering frequently occur during the growth and development of maize; however, the molecular mechanisms of heterosis under drought stress and re-watering have rarely been systematically investigated. Zhengdan7137 and Zhengdan7153 are two maize hybrid varieties with robust heterosis, and separately belongs to the SS×NSS and Reid×Tangsipingtou heterotic groups. 54 transcriptomes of these two hybrids and their parental inbred lines were analyzed under well-watering (WW), water-deficit (WD), and re-watering (RW) conditions using RNA-Seq. In this study, we identified 3,411 conserved drought response genes (CDRGs) and 3,133 conserved re-watering response genes (CRRGs) between Zhengdan7137 and Zhengdan7153. When comparing CDRGs and CRRGs to overdominance and underdominance genes, we identified 303 and 252 conservative drought response overdominance genes (DODGs) and underdominance genes (DUDGs), respectively, and 165 and 267 conservative re-watering response overdominance genes (RODGs) and underdominance genes (RUDGs), respectively. DODGs are involved in stress response-related processes, such as L-phenylalanine metabolism, carbohydrate metabolism, and heat response, whereas DUDGs are associated with glucose metabolism, pentose-phosphate shunt, and starch metabolism. RODGs and RUDGs contribute to the recovery of hybrids from drought stress by upregulating cell propagation and photosynthesis processes, and repressing stress response processes, respectively. It indicated overdominant and underdominant genes conservatively contributed to hybrid heterosis under drought stress. These results deepen our understanding of the molecular mechanisms of drought resistance, uncover conservative molecular mechanisms of heterosis under drought stress and re-watering, and provide potential targets for improving drought resistance in maize.

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.

Estimation of genetic components and assessing heterosis association with molecular markers in half diallel derived rice hybrids developed with landraces of NE India

Combining ability and heterosis were estimated in 45 rice hybrids generated by mating 10 parents, comprising both land races and advance breeding lines, in half diallel fashion. Hayman’s graphical analysis showed that all the twelve morphological traits studied had significant positive dominance variance. Narrow sense heritability was high for Days to fifty percentage flowering, Plant height, Panicle length and Test weight (> 30 %), and low for Grain yield per plant. According to the VrWr graph, traits like GYPP, PL, PH, TN and plot yield showed partial dominance, whereas traits like Blast disease index showed overdominance. A significant improvement over check was observed for heterosis and the crosses Mynri x CAUS103, Joha x CAUS107, CAUS 126 x CAUS107 and CAUS103 x CP, exhibited significantly positive standard heterosis for GYPP (>80 %) and PY (>100 %). Genetic distance based on fourteen markers revealed significant positive association with mid parent and better parent heterosis for Spikelet’s per plant, Filled grains per plant, Harvest index, Grain yield per plant, Panicle number and Plot yield. Therefore, it is evident that crosses with larger genetic distance between the parents gave hybrids with higher heterosis. Keywords: Landraces, Hayman’s graphical analysis, Heterosis, Genetic distance

Maximizing genetic gains across agronomic and consumer preference traits in St. Augustinegrass breeding

AbstractCombining large multi‐environment trial (MET) datasets to decide which genotypes to move forward in the breeding process can be challenging, especially when dealing with negatively correlated traits. The use of a selection index has long been identified as an effective strategy in these situations. However, the method has found limited application in turfgrass breeding. The objective of this study was to use MET data for St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] breeding lines evaluated across the southern United States to compare genetic gains achieved with the additive additive genetic index (AI) versus the turf performance index (TPI) incorporating agronomic as well as consumer preference traits. The use of either selection index produced more positive genetic gains across traits than direct selection even in the presence of negative correlations. However, the higher genetic gains obtained with AI versus TPI indicate that the use of an index that weighs traits according to their importance is a better approach for selection. Moreover, under a more stringent selection intensity, none of the best lines identified with AI would have been selected with TPI emphasizing the importance of choosing selection criteria that provide a more nuanced ranking of lines. Additionally, higher heritability values and gains from selection were obtained for turfgrass quality under stress (drought and shade) than under normal conditions indicating that selection under stress environments might be more efficient. Most of the evaluated St. Augustinegrass lines outperformed the checks, further supporting the value of cross‐institutional breeding collaborations.

Assessment of genetic variability, heritability and correlation in advanced breeding lines of bread wheat (Triticum aestivum) under heat stress condition

Abstract An experiment was conducted under normal (with six irrigation during crop period) and stressed condition during Rabi 2019 in All India Coordinated Research Project (AICRP) on Wheat, MARS, Dharwad, Karnataka with the view of assessing genetic variability, heritability and expected genetic advance in 104 F4 families of the cross HD2864 × DBW14. The progenies exhibited wide range of variation for all the traits indicating the presence of enough genetic variability in the material under study. Under timely sown condition, the traits like leaf waxyness, NDVI at different stages, SPAD at different stages, number of productive tillers per plant, seeds per spike, grain filling duration, spike length, thousand grains weight and seed set percentage showed high variability. The traits like plant height, canopy temperature at different stages and membrane stability index showed low variability. Under late sown condition, the traits like leaf waxyness, plant height, NDVI at different stages, SPAD at different stages, number of productive tillers per plant, seeds per spike, yield per plant, row bulk yield and seed set percentage showed high variability. The traits like days to maturity, spike length and membrane stability index showed low variability. The findings shows that all traits related to crop yield are positively linked, except for canopy temperature at different growth stages. Promising lines identified through Heat susceptibility index (HSI) and Heat tolerance index (HTI) can be utilized in future breeding programs to enhance crop productivity. Keywords: Variability, Coefficient of variation, Heritability, Genetic advance.

Accelerated reproduction of the parental lines of white cabbage using rosette plants (steckling) and artificial climate chambers

Relevance. The technology of producing cabbage seeds with the traditional method takes almost 2 years. Its high labor intensity caused the need to search for cheaper methods of selection and seed production. One of the ways to speed up the stages of the selection process is the use of artificial climate chambers. The aim of research is to obtain seeds of promising inbred lines of late maturing white cabbage and hybrid combinations with their participation using rosette plants (steckling) in artificial climate chambers. Materials and Methods. The material was inbred pure lines of 5-6 generations of inbreeding, obtained from promising hybrid combinations of domestic and foreign breeding. The research was conducted in 2023-2024. Sowing in Plantek 64 cassettes was carried out on July 10, then the seedlings were transplanted into vegetative vessels with an optimal volume of 5-6 liters and installed in the open ground for the growth of a leaf outlet. In the phase 10-13 of real leaves, the plugs were placed in an artificial climate chamber. During the growth and development period, biometric and phenological observations were carried out, and an analysis of seed setting was carried out during the hybridization of inbred lines.Results. As a result of research in the study of hybrid seed production under artificial climate chamber conditions, high rates of seed setting in buds under cross-pollination of rosette plants of white cabbage were revealed. Genotypes with high seed set rate under geitenogamous bud pollination were also identified. The weight of 1000 seeds of the studied plants was within the range of 2.5-5.14 g. Genotypes 383-3, 384-2 and 384-7 were selected, which had the highest percentage of seeds in the fractional composition with size more than 2 mm 80.3%, 43.5% and 59.4%, respectively. When genotypes 384-2 and 384-7 were used in hybrid combinations as a maternal component, high quality indicators of the obtained seeds were revealed.Conclusion. For the studied genotypes of white cabbage, when grown in an artificial climate chamber, no significant effect on seed quality was found; the genotype had a greater effect on seed quality indicators.

Foraging bee species differentially prioritize quantity and quality of floral rewards.

Pollinator-plant interactions represent a core mutualism that underpins biodiversity in terrestrial ecosystems, and the loss of flowering plants is a major driver of pollinator declines. Bee attraction to flowers is mediated by both quantity of resources (the number of available flowers for exploration) and quality of resources (pollen nutritional value), but whether and how bees prioritize these factors is not well understood. Here, we leveraged a unique plant system to investigate the floral factors influencing bee foraging decisions. Recombinant inbred plant lines were generated by crossing the self-fertilizing Capsella rubella and the pollinator-dependent outcrosser C. grandiflora, to produce plants that varied across floral traits. Using enclosed arenas, we evaluated the foraging behavior of two solitary bee species, Osmia cornifrons and Megachile rotundata, to the isolated inflorescences from these lines. Visits from O. cornifrons were significantly positively correlated with the number of flowers, while M. rotundata visits were significantly positively associated with pollen nutrition, with a preference for plants with higher pollen protein-to-lipid content. Further experiments using artificial flowers confirmed that M. rotundata preferred flowers with higher protein:lipid ratios, while O. cornifrons visits were unaffected by nutrition. These studies demonstrate that, although both bee species collect pollen as their sole source of protein and lipids for themselves and/or their offspring, they differentially prioritize resource quantity (number of flowers) and quality (pollen nutritional content). These studies lay the groundwork for understanding how different foraging strategies evolved, and influence, plant-pollinator ecological networks.

Genome-wide association study reveals genetic basis and candidate genes for chlorophyll content of leaves in maize (Zea mays L.).

The chlorophyll content (CC) directly affects photosynthesis, growth, and yield. However, the genetic basis of CC is still unclear in maize (Zea mays L.). Here, we conducted a genome-wide association study using mixed linear model for CC of the fifth leaves at seedling stage (CCFSS) and the ear leaves at filling stage (CCEFS) for 334 maize inbred lines. The heritability estimates for CCFSS and CCEFS, obtained via variance components analysis using the lme4 package in R, were 70.84% and 78.99%, respectively, indicating that the CC of leaves is primarily controlled by genetic factors. A total of 15 CC-related SNPs and 177 candidate genes were identified with a p-value < 4.49 × 10-5, which explained 4.98-7.59% of the phenotypic variation. Lines with more favorable gene variants showed higher CC. Meanwhile, Gene Ontology (GO) analysis implied that these candidate genes were probably related to chlorophyll biosynthesis. In addition, gene-based association analyses revealed that six variants in GRMZM2G037152, GRMZM5G816561, GRMZM2G324462, and GRMZM2G064657 genes were significantly (p-value < 0.01) correlated with CC, of which GRMZM2G064657 (encodes a phosphate transporter protein) and GRMZM5G816561 (encodes a cytochrome P450 protein) were specifically highly expressed in leaves tissues. Interestingly, these candidate genes were previously reported to involve in the regulation of the contents of chlorophyll in plants or Chlamydomonas. These results may contribute to the understanding of genetic basis and molecular mechanisms of maize CC and the selection of maize varieties with improved CC.

Allelic Diversity and Development of Breeder-Friendly Marker Specific to floury2 Gene Regulating the Accumulation of α-Zeins and Essential Amino Acids in Maize Kernel.

Maize zeins lack essential amino acids, such as methionine, lysine, and tryptophan. The floury2 (fl2) mutation reduces zein synthesis and increases methionine and lysine content in kernels. In this study, fl2 gene (1612bp) was sequenced in eight wild-type and two mutant inbreds and detected 218 SNPs and 18 InDels. Transversion of C to T at 343bp position caused the substitution of alanine by valine in the fl2 mutant. A PCR-based marker (FL-SNP-CT) was developed, which distinguished the favorable mutant fl2 allele (T) from the wild-type (C) Fl2 allele. Gene-based diversity analysis using seven gene-based InDel markers grouped 48 inbred lines into three major clusters, with an average genetic dissimilarity coefficient of 0.534. The average major allele frequency, gene diversity, heterozygosity, and polymorphism information content of the InDel markers were 0.701, 0.392, 0.039, and 0.318, respectively. Haplotype analysis revealed 29 haplotypes of fl2 gene among these 48 inbreds. Amino acid substitution (Ala-Val) at the signal peptide cleavage site produced unprocessed 24-kDa mutant protein instead of 22-kDa zein found in normal genotype. Eight paralogues of fl2 detected in the study showed variation in exon lengths (616-1170bp) and translation lengths (135-267 amino acids). Orthologue analysis among 15 accessions of Sorghum bicolor and two accessions of Saccharum spontaneum revealed a single exon in fl2 gene, ranging from 267 to 810bp. The study elucidated the molecular basis of fl2 mutation and reported a breeder-friendly marker for molecular breeding programs. This is the first study to characterize fl2 gene in a set of subtropically adapted inbreds.

Interactive effects of nitrogen and genotype on maize rough dwarf disease

AbstractNitrogen and genotype play vital roles in modulating plant disease resistance. Maize (Zea mays L.) rough dwarf disease (MRDD) is a global viral disease that has caused serious yield losses. However, it is not clear how nitrogen and genotype interact to affect MRDD. We conducted field experiments in 2011 and 2013 to investigate the MRDD incidence, yield, and yield loss rate of 59 maize hybrids under high nitrogen (HN) and low nitrogen (LN). Compared with HN, the MRDD incidence and yield loss rate of S‐sensitive hybrids (nitrogen significantly influenced MRDD incidence in susceptible genotypes) could be significantly reduced by 50.6% and 35.5%, respectively, in LN without compromising maize yield. In contrast, R‐insensitive types (resistant hybrids in which MRDD incidence was unresponsive to nitrogen treatment) could maintain high MRDD resistance and yield at HN. US hybrid 78599 and inbred line Dan340 were the main parental resources of the resistant genotypes, and inbred lines Huangzao4 and Ye478 were the main parental resources of the susceptible genotypes. The physiological mechanism leading to increased MRDD incidence was thought to be higher nitrogen concentrations in the stalks. This study provided theoretical support for using reasonable nitrogen management to control MRDD and breeding MRDD‐resistant maize hybrids.