Meta-QTL analysis for mining of candidate genes and constitutive gene network development for fungal disease resistance in maize(Zea mays L.)

The development of resistant maize cultivars is the most effective and sustainable approach to combat fungal diseases.Over the last three decades,many quantitative trait loci(QTL)mapping studies reported numerous QTL for fungal disease resistance(FDR)in maize.However,different genetic backgrounds of germplasm and differing QTL analysis algorithms limit the use of identified QTL for comparative studies.The meta-QTL(MQTL)analysis is the meta-analysis of multiple QTL experiments,which entails broader allelic coverage and helps in the combined analysis of diverse QTL mapping studies revealing common genomic regions for target traits.In the present study,128(33.59%)out of 381 reported QTL(from 82 studies)for FDR could be projected on the maize genome through MQTL analysis.It revealed 38 MQTL for FDR(12 diseases)on all chromosomes except chromosome 10.Five MQTL namely 1_4,2_4,3_2,3_4,and 5_4 were linked with multiple FDR.Total of 1910 candidate genes were identified for all the MQTL regions,with protein kinase gene families,TFs,pathogenesis-related,and disease-responsive proteins directly or indirectly associated with FDR.The comparison of physical positions of marker-traits association(MTAs)from genome-wide association studies with genes underlying MQTL interval verified the presence of QTL/candidate genes for particular diseases.The linked markers to MQTL and putative candidate genes underlying identified MQTL can be further validated in the germplasm through marker screening and expression studies.The study also attempted to unravel the underlying mechanism for FDR resistance by analyzing the constitutive gene network,which will be a useful resource to understand the molecular mechanism of defense-response of a particular disease and multiple FDR in maize.

Surveying the genomic landscape of silage-quality traits in maize(Zea mays L.)

Despite the longstanding importance of silage as a critical feed source for ruminants,its quality improvement has been largely overlooked.Although numerous quantitative trait loci(QTL)and genes affecting silage quality in maize have been reported,only a few have been effectively incorporated into breeding programs.Addressing this gap,the present study undertook a comprehensive meta-QTL(MQTL)analysis involving 523 QTL associated with silage-quality traits collected from 14 published studies.Of the 523 QTL,405 were projected onto a consensus map comprising 62,424 genetic markers,resulting in the identification of 60 MQTL and eight singletons.The average confidence interval(CI)of the MQTL was 3.9-fold smaller than that of the source QTL.Nine of the 60 identified MQTL were classified as breeder’s MQTL owing to their small CIs,involvement of more QTL,and large contribution to phenotypic variation.One-third of the MQTL co-localized with DNA marker-trait associations identified in previous genomewide association mapping studies.A set of 78 high-confidence candidate genes influencing silage quality were identified in the MQTL regions.These genes and associated markers may advance marker-assisted breeding for maize silage quality.

Genetic dissection of crown root traits and their relationships with aboveground agronomic traits in maize

The crown root system is the most important root component in maize at both the vegetative and reproductive stages. However, the genetic basis of maize crown root traits(CRT) is still unclear, and the relationship between CRT and aboveground agronomic traits in maize is poorly understood. In this study, an association panel including 531 elite maize inbred lines was planted to phenotype the CRT and aboveground agronomic traits in different field environments. We found that root traits were significantly and positively correlated with most aboveground agronomic traits, including flowering time, plant architecture and grain yield. Using a genome-wide association study(GWAS)coupled with resequencing, a total of 115 associated loci and 22 high-confidence candidate genes were identified for CRT. Approximately one-third of the genetic variation in crown root was co-located with 46 QTLs derived from flowering and plant architecture. Furthermore, 103 (89.6%) of 115 crown root loci were located within known domestication-and/or improvement-selective sweeps, suggesting that crown roots might experience indirect selection in maize during domestication and improvement. Furthermore, the expression of Zm00001d036901, a high-confidence candidate gene, may contribute to the phenotypic variation in maize crown roots, and Zm00001d036901 was selected during the domestication and improvement of maize. This study promotes our understanding of the genetic basis of root architecture and provides resources for genomics-enabled improvements in maize root architecture.

Physiological and Biochemical Effects of 24-Epibrassinolide on Heat-Stress Adaptation in Maize (Zea mays L.)

Brassinosteroids (BRs) are a family of about 70 structurally related polyhydroxy steroidal phytohormones that regulate a number of physiological processes in plants. Among these, brassinolide (BL), 28-homobrassinolide (28-homoBL) and 24-epibrassinolide (24-EpiBL) are more common. The present study aims at studying the usefulness of 24-epiBL in ameliorating the impacts of heat-stress in maize along with its role in regulating cellular antioxidant defense system. Maize hybrid PMH 3 was grown in pots in a green house maintained at 14 hours day (25℃)/10hours night (17℃). A solution of 24-epiBL (1 μM) was applied externally at V4 stage. Leaf tissues were sampled from both treated and control plants. Subsequently, both the groups of pots were placed in plant growth chamber maintained at high temperature (48℃;RH 50%). Plants were sampled for biochemical analysis after 3, 6, 9, 24 and 48 hours of high temperature exposure. Exogenous application of 24-EpiBL arrested protein degradation and enhanced cell membrane stability, as compared to the control. The biochemical activities of antioxidant enzymes such as catalase (CAT), superoxide dismutase (SOD) and peroxidase (POX) were found to be dynamically and variably modulated post 24-epiBL treatment. Thus, the study supports the role of BRs as anti-stress agents.

Identification and functional analysis of miRNAs in developing kernels of a viviparous mutant in maize

Given the important roles of miRNAs in post-transcriptional gene regulation, identification of differentially expressed miRNAs will facilitate the elucidation of molecular mechanisms underlying kernel development. In this study, we constructed a small RNA library to comprehensively represent the full complement of individual small RNAs and to characterize miRNA expression profiles in pooled ears of maize(Zea mays L.) at 10, 15,20, 22, 25 and 30 days after pollination(DAP). At least 21 miRNAs were differentially expressed. The differential expression of three of these miRNAs, i.e., miR528a, miR167a and miR160b, at each stage was verified by qRT-PCR. The results indicated that these miRNAs might be involved in kernel development. In addition, the predicted functions of target genes indicated that most of the target genes are involved in signal transduction and cell communication pathways, particularly the auxin signaling pathway. The expression of candidate germination-associated miRNAs was analyzed by hybridization to a maize genome microarray, and revealed differential expression of genes involved in plant hormone signaling pathways. This finding suggests that phytohormones play a critical role in the development of maize kernels. We found that in combination with other miRNAs, miR528a regulated a putative laccase, a Ring-H2 zinc finger protein and a MADS box-like protein, whereas miR167a and miR160b regulated multiple target genes,including ARF(auxin response factor), a member of the B3 transcription factor family. All three miRNAs are important for ear germination, development and physiology. The small RNA transcriptomes and mRNA obtained in this study will help us gain a betterunderstanding of the expression and function of small RNAs in the development of maize kernel.

Distribution,Etiology,Molecular Genetics and Management Perspectives of Northern Corn Leaf Blight of Maize(Zea mays L.)

Maize is cultivated extensively throughout the world and has the highest production among cereals.However,Northern corn leaf blight(NCLB)disease caused by Exherohilum turcicum,is the most devastating limiting factor of maize production.The disease causes immense losses to corn yield if it develops prior or during the tasseling and silking stages of crop development.It has a worldwide distribution and its development is favoured by cool to moderate temperatures with high relative humidity.The prevalence of the disease has increased in recent years and new races of the pathogen have been reported worldwide.The fungus E.turcicum is highly variable in nature.Though different management strategies have proved effective to reduce economic losses from NCLB,the development of varieties with resistance to E.turcicum is the most efficient and inexpensive way for disease management.Qualitative resistance for NCLB governed by Ht genes is a race-specific resistance which leads to a higher level of resistance.However,some Ht genes can easily become ineffective under the high pressure of virulent strains of the pathogen.Hence,it is imperative to understand and examine the consistency of the genomic locations of quantitative trait loci for resistance to NCLB in diverse maize populations.The breeding approaches for pyramiding resistant genes against E.turcicum in maize can impart NCLB resistance under high disease pressure environments.Furthermore,the genome editing approaches like CRISPR-cas9 and RNAi can also prove vital for developing NCLB resistant maize cultivars.As such this review delivers emphasis on the importance and current status of the disease,racial spectrum of the pathogen,genetic nature and breeding approaches for resistance and management strategies of the disease in a sustainable manner.

Chromosome-level genome assembly of Cylas formicarius provides insights into its adaptation and invasion mechanisms

Cylasformicarius is one of the most important pests of sweet potato worldwide, causing considerable ecological and economic damage.This study improved the effect of comprehensive management and understanding of genetic mechanisms by examining the functional genomics of C. formicarius.Using Illumina and PacBio sequencing, this study obtained a chromosome-level genome assembly of adult weevils from lines inbred for 15 generations.The high-quality assembly obtained was 338.84 Mb, with contig and scaffold N50 values of 14.97 and 34.23 Mb, respectively.In total, 157.51 Mb of repeat sequences and 11 907 protein-coding genes were predicted.A total of 337.06 Mb of genomic sequences was located on the 11 chromosomes, accounting for 99.03%of the total length of the associated chromosome.Comparative genomic analysis showed that C. formicarius was sister to Dendroctonus ponderosae, and C. formicarius diverged from D. ponderosae approximately 138.89 million years ago (Mya).Many important gene families expanded in the C. formicarius genome were involved in the detoxification of pesticides, tolerance to cold stress and chemosensory system.To further study the role of odorant-binding proteins (OBPs) in olfactory recognition of C. formicarius, the binding assay results indicated that Cfor OBP4–6 had strong binding affinities for sex pheromones and other ligands.The high-quality C. formicarius genome provides a valuable resource to reveal the molecular ecological basis, genetic mechanism, and evolutionary process of major agricultural pests;it also offers new ideas and new technologies for ecologically sustainable pest control.

Heat-tolerant maize for rainfed hot,dry environments in the lowland tropics:From breeding to improved seed delivery

Climate change-induced heat stress combines two challenges:high day-and nighttime temperatures,and physiological water deficit due to demand-side drought caused by increase in vapor-pressure deficit.It is one of the major factors in low productivity of maize in rainfed stress-prone environments in South Asia,affecting a large population of smallholder farmers who depend on maize for their sustenance and livelihoods.The International Maize and Wheat Improvement Center(CIMMYT)maize program in Asia,in partnership with public-sector maize research institutes and private-sector seed companies in South Asian countries,is implementing an intensive initiative for developing and deploying heat-tolerant maize that combines high yield potential with resilience to heat and drought stresses.With the integration of novel breeding tools and methods,including genomics-assisted breeding,doubled haploidy,fieldbased precision phenotyping,and trait-based selection,new maize germplasm with increased tolerance to heat stress is being developed for the South Asian tropics.Over a decade of concerted effort has resulted in the successful development and release of 20 high-yielding heat-tolerant maize hybrids in CIMMYT genetic backgrounds.Via public–private partnerships,eight hybrids are presently being deployed on over 50,000 ha in South Asian countries,including Bangladesh,Bhutan,India,Nepal,and Pakistan.

Effects of Long-term Fertilization on Soil M icrobial Com m unity Structure,Labile Organic Carbon and Nitrogen and Enzym e Activity in Paddy Field and Upland

To investigate the effects of long-term fertilization systems on soil microbial community structure,labile organic carbon and nitrogen and enzyme activity in yellow sand paddy field and upland,a field experiment was conducted at the experimental station of Dongyang Institute of Maize Research in Zhejiang Province,China in 2009.The experiment consisted of six treatments with three replicates,and they were arranged in a completely randomized design,including no fertilization in paddy field (PCK),conventional fertilization in paddy field (PCF),formulated fertilization by soil testing in paddy field (PSTF),formulated fertilization by soil testing with organic manure in paddy field (PSTF+OF),conventional fertilization on upland (DCF),and formulated fertilization by soil testing with organic manure on upland (DSTF+OF).Soil nutrients,enzyme activity,microbial biomass and community structure were determined in 2015.The results showed that compared with no fertilization in paddy field (PCK),fertilization increased soil phosphorus and potassium content,and decreased pH value.No fertilization in paddy field (PCK) had no significant effect on soil culturable microorganisms in paddy field and upland,but formulated fertilization by soil testing with organic manure on upland (DSTF+OF) significantly increased the number of fungi.Formula fertilization by soil testing with organic manure (PSTF+OF) also significantly increased soil microbial biomass carbon and nitrogen in paddy field and upland.Moreover,fertilization had no significant effect on soil cellulase activity,but formula fertilization by soil testing with organic manure (PSTF+OF) significantly increased soil dehydrogenase and catalase activity.Therefore,long-term application of chemical fertilizer with organic fertilizer can effectively improve soil fertility.

Study on Haploid Induction Rates in Different Maize Inducers

[Objective] The aim was to analyze the differences in haploid induction rates of different inducers. [Method] Six maize inducers with purple spot and purple color were selected as the male parents to pollinate six inbred lines. [Result] The mean haploid induction rates were significantly different among the inducers: KMS-3 >WY-1 >PR-2 >YP-13 >KMS-2 >KMS-1. The haploid induction rates of the different hybrid materials were significantly different: K410 >105A >103A >104A >107A >D271 >106A>L73>N21>KZ58. [Conclusion] The haploid inducer line PR-2, which had high haploid induction rate and low variation coefficient, was an elite haploid inducer.

Genetic gains with genomic versus phenotypic selection for drought and waterlogging tolerance in tropical maize(Zea mays L.)

Erratic rainfall often results in intermittent drought and/or waterlogging and limits maize(Zea mays L.)productivity in many parts of the Asian tropics.Developing climate-resilient maize germplasm possessing tolerance to these key abiotic stresses without a yield penalty under optimal growing conditions is a challenge for breeders working in stress-vulnerable agro-ecologies in the region.Breeding stress-resilient maize for rainfed stress-prone ecologies is identified as one of the priority areas for CIMMYT-Asia maize program.We applied rapid cycle genomic selection(RCGS)on two multiparent yellow synthetic populations(MYS-1 and MYS-2)to improve grain yield simultaneously under drought and waterlogging conditions using genomic-estimated breeding values(GEBVs).Also,the populations were simultaneously advanced using recurrent phenotypic selection(PS)by exposing them to managed drought and waterlogging and intermating tolerant plants from the two selection environments.Selection cycles per se(C1,C2,and C3)of the two populations developed using RCGS and PS approach and their test-cross progenies were evaluated separately in multilocation trials under managed drought,waterlogging,and optimal moisture conditions.Significant genetic gains were observed with both GS and PS,except with PS in MYS-2 under drought and with GS in MYS-1 under waterlogging.Realized genetic gains from GS were relatively higher under drought conditions(110 and 135 kg ha^(-1) year^(-1))compared to waterlogging(38 and 113 kg ha^(-1) year^(-1))in both MYS-1 and MYS-2,respectively.However,under waterlogging stress PS showed at par or better than GS as gain per year with PS was 80 and 90 kg ha^(-1),whereas with GS it was 90 and 43 kg ha^(-1) for MYS-1 and MYS-2,respectively.Our findings suggested that careful constitution of a multiparent population by involving trait donors for targeted stresses,along with elite highyielding parents from diverse genetic background,and its improvement using RCGS is an effective breeding approach to build multiple stress tolerance without compromising yield when tested under optimal conditions.

Predicting Yield and Stability Analysis of Wheat under Different Crop Management Systems across Agro-Ecosystems in India

The objectives of the study were as follows: 1) to evaluate the GxExM for wheat genotypes;2) to predict yield performance and identify high stable wheat genotypes in different management practices;and 3) to make genotype-specific management and high performing genotype recommendations within and across agro-ecological regions. A diverse set of twenty-one genotypes was evaluated over three years (2012, 2013 and 2014) under two levels of crop management practices (CT and ZT) across three agro-ecological regions (BR, MP and PB) of India in replicated trials. Data were analyzed with SASGxE and RGxE programs using SAS and R programming languages, respectively. Across and within a location(s), the pattern of GxExM and GxMxY interactions (respectively) among univariate and multivariate stability statistics, grouping of genotypes in divisive clusters and estimates (with a prediction interval) of genotype varied in management practice CT and ZT. Across locations, the genotypes “Munal” and “HD-2967” were the best performers and high stable in CT and ZT, respectively. Genotypes “HD-2824” and “DPW-621-50”, and “Munal” may serve as diverse parents for developing high quality, climate smart, locally adapted genotypes for BR in CT and ZT, respectively. Genotypes “HD-2932”, “BAZ” and “JW-3288”, and “GW-322” and “HD-2967” are suitable for developing locally adapted stress tolerant genotypes for MP in management practices CT and ZT, respectively. Relatively small GxM and GxExM interactions in PB preclude in making definitive conclusions.

Long-Term Conservation Agriculture and Intensified Cropping Systems:Effects on Growth,Yield,Water,and Energy-use Efficiency of Maize in Northwestern India

Conservation agriculture(CA)-based best-bet crop management practices may increase crop and water productivity, while conserving and sustaining natural resources. We evaluated the performance of rainy season maize during 2014 under an ongoing long-term trial(established in 2008) with three tillage practices, i.e., permanent bed(PB), zero tillage(ZT), and conventional tillage(CT) as main plots, and four intensified maize-based cropping systems, i.e., maize-wheat-mungbean, maize-chickpea-Sesbania(MCS), maizemustard-mungbean, and maize-maize-Sesbania) as subplot treatments. In the seventh rainy season of the experiment, maize growth parameters, yield attributes, yield, and water-and energy-use efficiency were highest at fixed plots under ZT. Maize growth parameters were significantly(P < 0.05) superior under ZT and PB compared with CT. Maize yield attributes, including cobs per m^2(7.8), cob length(0.183 m), grain rows per cob(13.8), and grains per row(35.6), were significantly higher under ZT than CT; however, no significant effect of cropping systems was found on maize growth and yield attributes. Zero tillage exhibited the highest maize productivity(4 589 kg ha^(-1)). However, among the cropping systems, MCS exhibited the highest maize productivity(4 582 kg ha^(-1)). In maize, water use was reduced by 80.2–120.9 mm ha-1under ZT and PB compared with CT, which ultimately enhanced the economic water-use efficiency by 42.0% and 36.6%, respectively. The ZT and PB showed a 3.5%–31.8% increase in soil organic carbon(SOC) at different soil depths(0–0.45 m), and a 32.3%–39.9% increase in energy productivity compared with CT. Overall, our results showed that CA-based ZT and PB practices coupled with diversified maize-based cropping systems effectively enhanced maize yield and SOC,as well as water-and energy-use efficiency, in northwestern India.

Analysis of the 3' ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

The purpose of this study was to investigate the characteristics of transfer RNA(tRNA) responsible for the association between tRNA genes and genes of apparently foreign origin(genomic islands) in five high-light adapted Prochlorococcus strains.Both bidirectional best BLASTP(basic local alignment search tool for proteins) search and the conservation of gene order against each other were utilized to identify genomic islands,and 7 genomic islands were found to be immediately adjacent to tRNAs in Prochlorococcus marinus AS9601,11 in P.marinus MIT9515,8 in P.marinus MED4,6 in P.marinus MIT9301,and 6 in P.marinus MIT9312.Monte Carlo simulation showed that tRNA genes are hotspots for the integration of genomic islands in Prochlorococcus strains.The tRNA genes associated with genomic islands showed the following characteristics:(1) the association was biased towards a specific subset of all iso-accepting tRNA genes;(2) the codon usages of genes within genomic islands appear to be unrelated to the codons recognized by associated tRNAs;and,(3) the majority of the 3' ends of associated tRNAs lack CCA ends.These findings contradict previous hypotheses concerning the molecular basis for the frequent use of tRNA as the insertion site for foreign genetic materials.The analysis of a genomic island associated with a tRNA-Asn gene in P.marinus MIT9301 suggests that foreign genetic material is inserted into the host genomes by means of site-specific recombination,with the 3' end of the tRNA as the target,and during the process,a direct repeat of the 3' end sequence of a boundary tRNA(namely,a scar from the process of insertion) is formed elsewhere in the genomic island.Through the analysis of the sequences of these targets,it can be concluded that a region characterized by both high GC content and a palindromic structure is the preferred insertion site.

A novel CCCH-type zinc finger protein SAW1 activates OsGA20ox3 to regulate gibberellin homeostasis and anther development in rice

Male sterility is a prerequisite for hybrid seed production.The phytohormone gibberellin(GA)is in-volved in regulating male reproductive development,but the mechanism underlying GA homeostasis in anther development remains less understood.Here,we report the isolation and characterization of a new positive regulator of GA homeostasis,swollen anther wall 1(SAW1),for anther development in rice(Oryza sativa L.).Rice plants carrying the recessive mutant allele saw1 produces abnormal anthers with swollen anther wall and aborted pollen.Clustered regularly interspaced short palindromic repeats(CRISPR)/CRIPSR-associated protein 9-mediated knockout of SAW1 in rice generated similar male sterile plants.SAW1 encodes a novel nucleus-localizing CCCH-tandem zinc finger protein,and this protein could directly bind to the promoter region of the GA synthesis gene OsGA20ox3 to induce its anther-specific expression.In the saw1 anther,the significantly decreased OsGA20ox3 expression resulted in lower bio-active GA content,which in turn caused the lower expression of the GA-inducible anther-regulator gene OsGAMYB.Thus,our results disclose the mechanism of the SAW1-GA20ox3-GAMYB pathway in controlling rice anther development,and provide a new target gene for the rapid generation of male sterile lines by genome editing for hybrid breeding.