QTL-allele matrix detected from RTM-GWAS is a powerful tool for studies in genetics, evolution, and breeding by design of crops

The plant germplasm resources harboring abundant genetic variations are necessary wealth in developing new cultivars adapted to various geographic and seasonal conditions.Unraveling the complex genetic architecture underlying phenotypic diversity in germplasm population is essential in studies on genetics,evolution and breeding plans for crop species.Mapping quantitative trait loci(QTLs)using molecular markers provide a basic tool for understanding the inheritance of quantitative traits,while the genomewide association study(GWAS)is a potential approach to detecting the whole-genome QTLs and their corresponding alleles in a germplasm population.The previous GWAS detects QTLs by taking high-density single-nucleotide polymorphism(SNP)markers to identify genotypephenotype associations,and has been extensively used for genetic dissection of quantitative traits in plants(Huang and Han 2014).

Corrigendum to“GmTOC1b negatively regulates resistance to Soybean mosaic virus”.[Crop J.11(2023)1762-1773]

The authors regret to report a mistake in the text and an associated change necessary to section 3.6 of the paper.On page 1766 in the right-hand column,line 4,the heading of subsection 3.6“GmWRKY40 represses the expression of PR genes”should be changed to“GmWRKY40 promotes the expression of PR genes”.The authors would like to apologize for any inconvenience caused.

The effect of integrative crop management on root growth and methane emission of paddy rice

In previous studies, integrative crop management (ICM) improved shoot growth and grain yield of rice (Oryza sativa L.). However, little is known about the effect of ICM on root growth and methane (CH4) emission of paddy rice. In this study, two rice varieties, Wuyunjing 24 and Yongyou 2640, were grown. A field experiment was conducted with three crop management treatments including zero nitrogen fertilization (0N), local farmer practice (LFP), and ICM. Root morphophysiological traits and CH4 emission from the paddy field were investigated. ICM significantly increased mean grain yield by 29.9%, with the effect attributed mainly to an increase in mean total number of spikelets by 26.4% compared to LFP. ICM increased root and shoot biomass, root length, number of roots, root oxidation activity (ROA), root bleeding rate, and root total and active absorbing surface area by respectively 24.4%, 25.7%, 17.1%, 9.3%, 18.7%, 29.5%, 12.1%, and 24.7%. The concentrations of malic, succinic, and acetic acids in root exudates were respectively 5.8%, 6.0%, and 10.5% higher in ICM than in LFP. Compared to LFP, ICM significantly decreased the rate of CH4 emission during emission peak stages and reduced total CH4 emission by 17.1%. The root morphophysiological traits were positively and significantly correlated with grain yield, whereas root length, specific root length, ROA, and root total and active absorbing surface area were negatively and significantly correlated with total CH4 emission. These results suggest that ICM could achieve the dual goals of increasing grain yield and reducing the greenhouse gas effect by improving the root morphology and physiological traits of paddy rice.

High-throughput phenotyping: Breaking through the bottleneck in future crop breeding

With the rapid development of genetic analysis techniques and crop population size,phenotyping has become the bottleneck restricting crop breeding.Breaking through this bottleneck will require phenomics,defined as the accurate,high-throughput acquisition and analysis of multi-dimensional phenotypes during crop growth at organism-wide levels,ranging from cells to organs,individual plants,plots,and fields.Here we offer an overview of crop phenomics research from technological and platform viewpoints at various scales,including microscopic,ground-based,and aerial phenotyping and phenotypic data analysis.We describe recent applications of high-throughput phenotyping platforms for abiotic/biotic stress and yield assessment.Finally,we discuss current challenges and offer perspectives on future phenomics research.

Genetic mapping of quantitative trait loci in crops

Dissecting the genetic architecture of complex traits is an ongoing challenge for geneticists.Two complementary approaches for genetic mapping,linkage mapping and association mapping have led to successful dissection of complex traits in many crop species.Both of these methods detect quantitative trait loci(QTL) by identifying marker–trait associations,and the only fundamental difference between them is that between mapping populations,which directly determine mapping resolution and power.Based on this difference,we first summarize in this review the advances and limitations of family-based mapping and natural population-based mapping instead of linkage mapping and association mapping.We then describe statistical methods used for improving detection power and computational speed and outline emerging areas such as large-scale meta-analysis for genetic mapping in crops.In the era of next-generation sequencing,there has arisen an urgent need for proper population design,advanced statistical strategies,and precision phenotyping to fully exploit high-throughput genotyping.

The genome sequence of celery(Apium graveolens L.),an important leaf vegetable crop rich in apigenin in the Apiaceae family

Celery(Apium graveolens L.)is a vegetable crop in the Apiaceae family that is widely cultivated and consumed because it contains necessary nutrients and multiple biologically active ingredients,such as apigenin and terpenoids.Here,we report the genome sequence of celery based on the use of HiSeq 2000 sequencing technology to obtain 600.8 Gb of data,achieving~189-fold genome coverage,from 68 sequencing libraries with different insert sizes ranging from 180 bp to 10 kb in length.The assembled genome has a total sequence length of 2.21 Gb and consists of 34,277 predicted genes.Repetitive DNA sequences represent 68.88%of the genome sequences,and LTR retrotransposons are the main components of the repetitive sequences.Evolutionary analysis showed that a recent whole-genome duplication event may have occurred in celery,which could have contributed to its large genome size.The genome sequence of celery allowed us to identify agronomically important genes involved in disease resistance,flavonoid biosynthesis,terpenoid metabolism,and other important cellular processes.The comparative analysis of apigenin biosynthesis genes among species might explain the high apigenin content of celery.The whole-genome sequences of celery have been deposited at CeleryDB(http://apiaceae.njau.edu.cn/celerydb).The availability of the celery genome data advances our knowledge of the genetic evolution of celery and will contribute to further biological research and breeding in celery as well as other Apiaceae plants.

Genomic selection methods for crop improvement:Current status and prospects

With marker and phenotype information from observed populations, genomic selection （GS） can be used to establish associations between markers and phenotypes. It aims to use genome-wide markers to estimate the effects of all loci and thereby predict the genetic values of untested populations, so as to achieve more comprehensive and reliable selection and to accelerate genetic progress in crop breeding. GS models usually face the problem that the number of markers is much higher than the number of phenotypic observations. To overcome this issue and improve prediction accuracy, many models and algorithms, including GBLUP, Bayes, and machine learning have been employed for GS. As hot issues in GS research, the estimation of non-additive genetic effects and the combined analysis of multiple traits or multiple environments are also important for improving the accuracy of prediction. In recent years, crop breeding has taken advantage of the development of GS. The principles and characteristics of current popular GS methods and research progress in hese methods for crop improvement are reviewed in this paper.

Sweet sorghum and Miscanthus：Two potential dedicated bioenergy crops in China

Among the potential non-food energy crops,the sugar-rich C4 grass sweet sorghum and the biomass-rich Miscanthus are increasingly considered as two leading candidates.Here,we outline the biological traits of these energy crops for largescale production in China.We also review recent progress on understanding of plant cell wall composition and wall polymer features of both plant species from large populations that affect both biomass enzymatic digestibility and ethanol conversion rates under various pretreatment conditions.We finally propose genetic approaches to enhance biomass production,enzymatic digestibility and sugar-ethanol conversion efficiency of the energy crops.

Heavy soil drying during mid-to-late grain filling stage of the main crop to reduce yield loss of the ratoon crop in a mechanized rice ratooning system

Yield loss(Y_(Loss)) in the ratoon crop due to crushing damage to left stubble from mechanical harvesting of the main crop is a constraint for wide adoption of mechanized rice ratooning technology.Soil drying before the harvest of the main crop has been proposed to overcome this problem.The objective of this study was to determine the effect of soil drying during the mid-to-late grain filling stage of the main crop on grain yield of the ratoon crop in a mechanized rice ratooning system.Field experiments were conducted to compare Y_(Loss) between light(LD) and heavy(HD) soil drying treatments in Hubei province,central China in 2017 and 2018.Y_(Loss) was calculated as the percentage of yield reduction in the ratoon crop with the main crop harvested mechanically,relative to the grain yield of the ratoon crop with the main crop harvested manually.In comparison with LD,soil hardness was increased by 42.8%-84.7% in HD at the 5-20 cm soil depth at maturity of the main crop.Soil hardness at 5 and 10 cm depths reached respectively 4.05 and 7.07 kg cm^(-2) in HD.Soil drying treatment did not significantly affect the grain yield of the main crop.Under mechanical harvesting of the main crop,HD increased the grain yield of the ratoon crop by 9.4% relative to LD.Consequently,Y_(Loss) was only 3.4% in HD,in contrast to 16.3% in LD.The differences in grain yield and Y_(Loos) between the two soil drying treatments were explained mainly by panicles m^(-2),which was increased significantly by HD in the track zone of the ratoon crop compared with LD.These results suggest that heavy soil drying practice during the mid-to-late grain filling stage of the main crop is effective for reducing Y_(Loss) of the ratoon crop in a mechanized rice ratooning system.

Arbuscular mycorrhizal fungi combined with exogenous calcium improves the growth of peanut(Arachis hypogaea L.)seedlings under continuous cropping

The growth and yield of peanut are negatively affected by continuous cropping.Arbuscular mycorrhizal fungi(AMF)and calcium ions(Ca^(2+))have been used to improve stress resistance in other plants,but little is known about their roles in peanut seedling growth under continuous cropping.This study investigated the possible roles of the AMF Glomus mosseae combined with exogenous Ca^(2+)in improving the physiological responses of peanut seedlings under continuous cropping.G.mosseae combined with exogenous Ca^(2+)can enhance plant biomass,Ca^(2+)level,and total chlorophyll content.Under exogenous Ca^(2+)application,the F_v/F_m in arbuscular mycorrhizal(AM)plant leaves was higher than that in the control plants when they were exposed to high irradiance levels.The peroxidase,superoxide dismutase,and catalase activities in AM plant leaves also reached their maximums,and accordingly,the malondialdehyde content was the lowest compared to other treatments.Additionally,root activity,and content of total phenolics and flavonoids were significantly increased in AM plant roots treated by Ca^(2+)compared to either G.mosseae inoculation or Ca^(2+)treatment alone.Transcription levels of AhCaM,AhCDPK,AhRAM1,and AhRAM2 were significantly improved in AM plant roots under exogenous Ca^(2+)treatment.This implied that exogenous Ca^(2+)might be involved in the regulation of G.mosseae colonization of peanut plants,and in turn,AM symbiosis might activate the Ca^(2+)signal transduction pathway.The combination of AMF and Ca^(2+)benefitted plant growth and development under continuous cropping,suggesting that it is a promising method to cope with the stress caused by continuous cropping.

Divergent evolutionary patterns of the MAPK cascade genes in Brassica rapa and plant phylogenetics

Mitogen-activated protein kinase(MAPK)cascade signal transduction modules play crucial roles in regulating many biological processes in plants.These cascades are composed of three classes of hierarchically organized protein kinases,MAPKKKs,MAPKKs and MAPKs.Here,we analyzed gene retention,phylogenetic,evolution and expression patterns of MAPK cascade genes in Brassica rapa.We further found that the MAPK branches,classes III and IV,appeared after the split of bryophytes and green algae after analyzing the MAPK cascade genes in 8 species,and their rapid expansion led to the great size of the families of MAPKs.In contrast,the ancestral class I subfamily of MAPKK gene families have been highly conserved from algae to angiosperms.For the MAPKKK family,the MEKK and Raf subfamily share a common evolutionary origin,and Raf plays a major role in the expansion of the MAPKKK gene family.The cis-elements and interaction network analyses showed the important function of MAPK cascade genes in development and stress responses in B.rapa.This study provides a solid foundation for molecular evolution analyses of MAPK cascade genes.

Effects of nitrogen management on the ratoon crop yield and head rice yield in South USA

Ratoon rice cropping is an important component of the rice cropping system in Texas and south Louisiana,USA,and expanded to Asian countries in 1970.Two field studies were conducted with widely planted rice(Oryza sativa L.)cultivars at Eagle Lake,Texas,USA to determine the effects of nitrogen(N)management in main(first)crop(MC)and ratoon(second)crop(RC)on RC yield.In 2012 and 2013,one cultivar(Presidio)was adopted to determine the effects of RC N management on ratoon yield and head rice yield.In 2016 and 2017,CL153,CL163 and CL272 in addition to Presidio were adopted to examine the effect of MC N management on ratoon yield and head rice yield.N applied at preflood after MC harvest considerably improved RC yield.Application of 99 kg N ha^(–1)at preflood after MC harvest was practically adequate for RC regrowth,development and approaching the yield potential for Presidio.RC could produce quite high average grain yields of 5.90 to 6.53 t ha–1 in 2012 and 2013,respectively.Main crop N rate only significantly affected MC yield;however,given N applied of 99 kg ha^(–1)at preflood after MC harvest,ratoon yield was not significantly affected by MC N rate.Neither the main nor ratoon crop N management had a significant effect on RC head rice yield.Considerable RC head rice yields(55–65%)were observed in all of the four cultivars and 4 years except for CL272 in 2016.These results indicat that without very high N fertilizer application,rice ratoon crop could produce a considerable grain yield and an expectative head rice yield.Rice ratooning could be a practical way to increase rice yields with the minimal input in south Texas and regions with a similar climate.

Border effects of the main and ratoon crops in the rice ratooning system

The border effect(BE)is widely observed in crop field experiments,and it has been extensively studied in many crops.However,only limited attention has been paid to the BE of ratoon rice.We conducted field experiments on ratoon rice in Qichun County,Hubei Province,Central China in 2018 and 2019 to compare the BE in the main and ratoon crops,and to quantify the contribution of BE in the main crop to that in the ratoon crop.The BE of two hybrid varieties was measured for the outermost,second outermost,and third outermost rows in each plot of both crops.To determine the contribution of BE between the two crops,portions of hills in the outermost and second outermost rows were uprooted during the harvest of the main crop so that the second and third outermost rows then became the outermost rows in the ratoon crop.Overall,the BE on grain yield was greater in the main crop than in the ratoon crop.In the main crop,the BE on grain yield was 98.3%in the outermost row,which was explained by the BE on panicles m^(–2),spikelets/panicle,spikelets m^(–2),and total dry weight.In the ratoon crop,the BE on grain yield was reduced to 60.9 and 27.6%with and without the contribution of the BE in the main crop,respectively.Consequently,55.1%of the BE on grain yield in the ratoon crop was contributed from the main crop.High stubble dry weight and non-structural carbohydrate(NSC)accumulation at the harvest of the main crop were responsible for the contribution of BE in the main crop to that in the ratoon crop.Our results suggest that increases in stubble dry weight and NSC accumulation at the harvest of the main crop could be important strategies for developing high-yielding cropping practices in the rice ratooning system.

Effects of plant density and mepiquat chloride application on cotton boll setting in wheat–cotton double cropping system

Sowing cotton directly after harvesting wheat in the Yangtze River Valley of China requires early mature of cotton without yield reduction.Boll-setting period synchronisation and more yield bolls distributed at the upper and middle canopy layers are also required for harvesting.The objective of this study is to quantify the individual and interaction effects of plant density and plant growth regulator mepiquat chloride(MC)on temporal and spatial distributions of yield bolls,as well as yield and yield components.During the 2013–2016 cotton growing seasons,the experiments were conducted on a shortseason cotton cultivar CRRI50 at Yangzhou University,China.Various combinations of plant density(12.0,13.5 and 15.0 plants m^(–2))and MC dose(180,270 and 360 g ha^(–1))were applied on cotton plants.The combination of 13.5 plants m^(–2)and 270 g ha^(–1)MC resulted in the greatest boll number per unit area,the highest daily boll setting number and more than 90%of bolls positioned within 45–80 cm above the ground.In conclusion,appropriate MC dose in combination of high plant density could synchronize boll-setting period and retain more bolls at the upper and middle canopy layers without yield reduction in the system of direct-seeded cotton after wheat harvest,and thus overcome the labor-intensive problem in current transplanting cropping system.

Cytogenetics and germplasm enrichment in Brassica allopolyploids in China

This paper reviews research advances in cytogenetics and germplasm innovation in Brassica allopolyploids, particularly oilseed rape（Brassica napus）, in China. Three naturally evolved Brassica allotetraploid species are cytologically stable but tend to preferentially lose several chromosomes from one subgenome when induced by alien chromosome elimination. A-subgenome is extracted from B. napus, and the ancestral Brassica rapa was restituted after the total loss of C-subgenome chromosomes. Genome-wide genetic and epigenetic alterations were observed in both natural and synthetic Brassica allotetraploids. B. napus was subjected to extensive interspecific hybridization with landraces of B. rapa and Brassica juncea, which exhibit abundant phenotype variations, to widen the genetic diversity in breeding and select numerous elite germplasm resources and cultivars; these cultivars include the representative Zhongyou 821, which also parented numerous other varieties. Novel B. napus genotypes were obtained using Brassica trigenomic hybrids and allohexaploids（2 n=54, AABBCC） by combining subgenomes from extant allotetraploids and diploids as bridge. Alien additions, substitutions, and translocations of the B. napus genome were developed by intergeneric/intertribal sexual and somatic hybridizations with several crucifers. Furthermore, mitochondrial DNA recombination promoted the production of novel cytoplasmic male sterile lines.

Effects of Genetics and Environment on Fatty Acid Stability in Soybean Seed

Although seed oil production and composition are genetically controlled, changes of oil level and oil composition across genotypes and environments such as drought and temperature were observed. The mechanisms of how genotypes interact with environment, affecting oil production and composition, are still not well understood. The objective of this research was to investigate the effect of drought/water stress and temperature on soybean genotypes. Two soybean genotypes of maturity group (MG) II (PI 597411 B and PI 597408) and two of MG VI (Arksoy and PI 437726) were used. A repeated greenhouse experiment to study the effect of water stress and a repeated growth chamber experiment to study the effect of temperature were conducted. The results showed that both water stress and high temperature altered seed oil composition by increasing oleic acid and decreasing linoleic and linolenic acid concentrations. Severe water stress (soil water potential between -150 to -200 kPa) or high temperature (40/33℃, day/night) resulted in higher palmitic acid and lower stearic acid. Genotypes differed in their responses to water stress or temperature. Analyses of seed carbohydrates (glucose, fructose, sucrose, raffinose, and stachyose) showed a significant decline of glucose, fructose, and sucrose and a significant increase of stachyose concentration by water stress and high temperature. Analyses of natural abundance of δ15N and δ13C isotopes showed changes in sources of nitrogen and carbon fixation, possibly affecting nitrogen and carbon metabolism pathways. The research demonstrated that both water stress and high temperature altered oil production and composition, and this could be partially related to limited availability and movement of carbohydrates from leaves to seed. Further research to investigate the enzymes controlling fatty acids conversion and nitrogen and carbon metabolism is needed.

The effects of soil properties, cropping systems and geographic location on soil prokaryotic communities in four maize production regions across China

The diversity of prokaryotic communities in soil is shaped by both biotic and abiotic factors.However,little is known about the major factors shaping soil prokaryotic communities at a large scale in agroecosystems.To this end,we undertook a study to investigate the impact of maize production cropping systems,soil properties and geographic location(latitude and longitude)on soil prokaryotic communities using metagenomic techniques,across four distinct maize production regions in China.Across all study sites,the dominant prokaryotes in soil were Alphaproteobacteria,Gammaproteobacteria,Betaproteobacteria,Gemmatimonadetes,Acidobacteria,and Actinobacteria.Non-metric multidimensional scaling revealed that prokaryotic communities clustered into the respective maize cropping systems in which they resided.Redundancy analysis(RDA)showed that soil properties especially pH,geographic location and cropping system jointly determined the diversity of the prokaryotic communities.The functional genes of soil prokaryotes from these samples were chiefly influenced by latitude,soil pH and cropping system,as revealed by RDA analysis.The abundance of genes in some metabolic pathways,such as genes involved in microbe–microbe interactions,degradation of aromatic compounds,carbon fixation pathways in prokaryotes and microbial metabolism were markedly different across the four maize production regions.Our study indicated that the combination of soil pH,cropping system and geographic location significantly influenced the prokaryotic community and the functional genes of these microbes.This work contributes to a deeper understanding of the composition and function of the soil prokaryotic community across large-scale production systems such as maize.

Drought-responsive genes expressed predominantly in root tissues are enriched with homotypic cis-regulatory clusters in promoters of major cereal crops

The root appears to be the most relevant organ for breeding drought stress tolerance.However, our knowledge about temporal and spatial regulation of drought-associated genes in the root remains fragmented, especially in crop plants. We performed a meta-analysis of expression divergence of essential drought-inducible genes and analyzed their association with cis-elements in model crops and major cereal crops. Our analysis of42 selected drought-inducible genes revealed that these are expressed primarily in roots,followed by shoot, leaf, and inflorescence tissues, especially in wheat. Quantitative real-time RT-PCR analysis confirmed higher expression of TaDREB2 and TaAQP7 in roots,correlated with extensive rooting and drought-stress tolerance in wheat. A promoter scan up to 2 kb upstream of the translation start site using phylogenetic footprinting revealed708 transcription factor binding sites, including drought response elements(DREs), auxin response elements(Aux REs), MYCREs/MYBREs, ABAREs, and ERD1 in 19 selected genes.Interestingly, these elements were organized into clusters of overlapping transcription factor binding sites known as homotypic clusters(HCTs), which modulate drought physiology in plants. Taken together, these results revealed the expression preeminence of major drought-inducible genes in the root, suggesting its crucial role in drought adaptation. The occurrence of HCTs in drought-inducible genes highlights the putative evolutionary modifications of crop plants in developing drought adaptation. We propose that these DNA motifs can be used as molecular markers for breeding drought-resilient cultivars, particularly in the cereal crops.

The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

Grapevine is one of the most economically important crops worldwide.However,the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres,limiting the accessibility of the repetitive sequences,the centromeric and telomeric regions,and the study of inheritance of important agronomic traits in these regions.Here,we assembled a telomere-to-telomere(T2T)gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads.The T2T reference genome(PN_T2T)is 69 Mb longer with 9018 more genes identified than the 12X.v0 version.We annotated 67%repetitive sequences,19 centromeres and 36 telomeres,and incorporated gene annotations of previous versions into the PN_T2T assembly.We detected a total of 377 gene clusters,which showed associations with complex traits,such as aroma and disease resistance.Even though PN40024 derives from nine generations of selfing,we still found nine genomic hotspots of heterozygous sites associated with biological processes,such as the oxidation–reduction process and protein phosphorylation.The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.

Current Situations of Competitive Scientific Research Projects for Agri-scientific Research Institutions: A Case Study of Tropical Crops Genetic Resources Institute of Chinese Academy of Tropical Agricultural Sciences

This paper collected and arranged competitive scientific research projects undertaken by Tropical Crops Genetic Resources Institute of Chinese Academy of Tropical Agricultural Sciences in 2003-2014. Through statistical analysis on quantity of projects,funded amount,age of person responsible,professional title of person responsible,academic degree of person responsible,research object,it discussed relevant characteristics and rules. Finally,it came up with pertinent measures and recommendations,in the hope of providing services for decision-making and scientific and technological management.