Epistasis-aware genome-wide association studies provide insights into the efficient breeding of high-yield and high-quality rice

Marker-assisted selection(MAS)and genomic selection(GS)breeding have greatly improved the efficiency of rice breeding.Due to the influences of epistasis and gene pleiotropy,ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.In this study,113 indica rice varieties(V)and their 565 testcross hybrids(TC)were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.The original traits and general combining ability of the parents,as well as the original traits and midparent heterosis of TC,were subjected to genome-wide association analysis.In total,381 primary significantly associated loci(SAL)and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.Among these loci,322 candidate genes located within or nearby the SALs were screened,204 of which were cloned genes.A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.All the SALs were used to construct genetic networks,in which 91 pleiotropic loci were investigated.Additionally,we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs,primary SALs,secondary SALs or epistatic effect SALs as covariates.Although the prediction accuracies of the four models were generally not significantly different in the TC dataset,the incorporation of primary SALs,secondary SALs,and epistatic effect SALs significantly improved the prediction accuracies of 5(26%),3(16%),and 11(58%)traits in the V dataset,respectively.These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice.

Induction of Tolerance to Fusarium Wilt and Defense-Related Mechanisms in the Plantlets of Susceptible Berangan Banana Pre-Inoculated with Pseudomonas sp.(UPMP3) and Burkholderia sp.(UPMB3)

This study is aimed at assessing the ability of two endophytic bacteria originally isolated from healthy oil palm roots, Pseudomonas sp. （UPMP3） and Burkholderia sp. （UPMB3） to induce resistance in susceptible Berangan banana against Fusarium oxysporum race 4 （FocR4）. Increased accumulation of resistance-related enzymes such as peroxidase （PO）, phenylalanine ammonia lyase （PAL）, lignithioglycolic acid （LTGA）, and pathogenesis-related （PR） proteins （ehitinase and β-1,3-glucanase） has been observed in plantlets treated with endophytic bacteria UPMP3 and UPMB3 singly or as mixture under glasshouse conditions. Pre-inoculation of banana plantlets with UPMP3 showed a significant reduction in Fusarium wilt incidence 72 d after challenged inoculation with FocR4. UPMB3 was less effective in suppressing Fusarium wilt compared to UPMP3, whereas, the mixture of both endophytes showed an intermediate effect. Based on these results, it is concluded that UPMP3 could be a promising biological control agent that can trigger resistance against Fusarium wilt in susceptible Berangan banana.

Effect of Seed Bacterization on Plant Growth Response and Induction of Disease Resistance in Chilli

This study aimed to examine the induction of disease resistance, and growth response in chilli plants elicited by plant growth promoting endophytic bacteria [Pseudomonas aeruginosa （UPMP3）, Burkholderia cepacia （UPMB3）, and Serratia marcescens （UPMS3）]. Seed bacterization with UPMP3 and UPMB3 significantly increased peroxidase （PO）, polyphenol oxidase （PPO）, and phenylalanine ammonia-lyase （PAL） activities. This increase corresponded to greater reduction in pre-and post-emergence damping-off caused by Sclerotium rolfsii. UPMS3 alone or as mixture with UPMP3 and UPMB3 did not show any significant reduction in disease incidence. However, all the isolates tested did not inhibit the seed germination and seedling establishment in chilli.

Chromosome-level genomes of seeded and seedless date plum based on third-generation DNA sequencing and Hi-C analysis

Diospyros lotus L.(Date plum)is an important tree species that produces fruit with a high nutritional value.An accurate chromosomal assembly of a species facilitates research on chromosomal evolution and functional gene mapping.In this study,we assembled the first chromosome-level genomes of seeded and seedless D.lotus using Illumina short reads,PacBio long reads,and Hi-C technology.The assembled genomes comprising 15 chromosomes were 617.66 and 647.31 Mb in size,with a scaffold N50 of 40.72 and 42.67 Mb for the seedless and seeded D.lotus,respectively.A BUSCO analysis revealed that the seedless and seeded D.lotus genomes were 91.53% and 91.60%complete,respectively.Additionally,20,689(95.4%)and 22,844(98.5%)protein-coding genes in the seedless and seeded D.lotus genomes were annotated,respectively.Comparisons of the chromosomes between genomes revealed inversions and translocations on chromosome 8 and inversions on chromosome 11.We identified 490 and 424 gene families that expanded in the seedless and seeded D.lotus,respectively.The enriched pathways among these gene families included the estrogen signaling pathway,the MAPK signaling pathway,and biosynthetic pathways for flavonoids,monoterpenoids,and glucosinolates.Moreover,we constructed the first Diospyros genome database(http://www.persimmongenome.cn).On the basis of our data,we developed the first high-quality annotated D.lotus reference genomes,which will be useful for genomic studies on persimmon and for clarifying the molecular mechanisms underlying important traits.Comparisons between the seeded and seedless D.lotus genomes may also elucidate the molecular basis of seedlessness.

Screening of Bacillus subtilis HAAS01 and Its Biocontrol Effect on Fusarium wilt in Sweet Potato

Fusarium wilt,a disease caused by Fusarium oxysporum f.sp batatas(Fob)is an important disease in sweet potato production.Using endophytic bacteria for biological control of sweet potato diseases is one of the important ways.A Bacillus subtilis with antagonistic effect on Fusarium wilt of sweet potato was isolated from soil by confrontation culture.According to the biological characteristics,16S rDNA sequence analysis,and physiological and biochemical analysis,the Bacillus subtilis HAAS01 was named.A pot experiment was conducted for the biological control experiment of strain HAAS01,and the endogenous hormone content,antioxidant enzyme activity,soluble protein content,and related gene expressions of sweet potato plants were detected.The results showed that the HAAS01 strain could promote the production of endogenous hormones and resist the infection of plant diseases together with defensive enzymes and upregulation of related gene expressions.In summary,Bacillus subtilis HAAS01 was effective in controlling Fusarium wilt of sweet potato and has potential for application and development.

Characteristics of High Quality Rice Xiang 5 and the Supporting Cultivation Techniques

The high quality rice,Xiang 5,is a new strain bred by Institute of Food Crops of Hubei Academy of Agricultural Sciences which first hybridizes Chinese scented rice with 9311,and then re-crosses it with Ezhong 5 for continuous generations. The strain has good quality,high yield,suitable maturity period,strong scent,strong combining ability and other features. This paper summarizes the appearance characteristics of Xiang 5 and main points of the supporting cultivation techniques,aimed at providing technical support and theoretical reference for its field production.

Growth and Development of Callosobruchus chinensis L.(Coleoptera:Bruchidae) on Different Beans

[ Objective ] The paper was to study the growth and development characteristics of Callosobruchus chinensis L. on different beans, and to explore the resistance of different beans to C. chiaensis. [ Method] The egg hatchability, growth and development of larva and adult of C. chinensis L. on different beans were observed in the laboratory at 30℃. [ Result] All the eight kinds of beans were spawned, but there were differences in egg hatchability among different beans. The egg hatchahility on Vigna radiate was the highest of （78.47 ±6.70） %. After hatching, larvae only drilled into grains of V. radiate, Vigna umbellate, Vicia faba, Pisum sativum and Cicer arietiaum, but there were significant differences in generation survival rate. The generation survival rate on V. radiate was the highest of （68.75 ±9.08）% and that on 1/. faba was the lowest of （26.93± 10.28 ）%. The development duration of C. chinensis on V. radiate was the shortest of （34.78 ± 2.02）d; the intrinsic rate of increase and finite rate of increase were greater of 0. 041 09 and 1. 041 95, respectively. [ Conclusion] A large number of C. chinertsis could be reproduced within a short period if feeding on V. radiate.

Preliminary Study on the Waterlogging Tolerance of 116 Corn Materials

Maize is one of the most important food crops in the world.With the global warming,waterlogging stress has become an important abiotic stress factor that affects crop growth,including maize.Waterlogging seriously affects 10%of the arable land and can lead to a 15%-80%reduction in crop yield[1].In this study,115 inbred line materials commonly used in spring maize planting areas in the Jianghan Plain,Hubei,and maize inbred line B73 with complete genome information,were collected and stressed by waterlogging for two weeks in the seven-leaf and one-heart stage,and the survival rate was statistically compared and analyzed,aiming to screen germplasms with strong waterlogging tolerance for the genetic improvement of waterlogging tolerance of Hubei maize lines.

Assessment of <i>Stevia rebaudiana</i>Bertoni Genotypes via Morpho-Agronomic Traits under Two Light Conditions

Stevia rebaudiana Bertoni, a non caloric natural sweetner is currently the available substitute to sugar. It is a genus of about 150 species of herbs and shrubs, a compositae and native to Paraguay. However, stevia is a short day plant with almost a constant day length 12 hours in Malaysia stevia generated to flower early. Therefore, the aim of the study was to investigate the effect of different day length on Stevia rebaudiana genotypes in Malaysia. The experiment was undertaken during December 2016 to April 2017 in the Faculty of Design and Architecture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia. Eight stevia genotypes namely (CHV1, Morita2, MS012, MS012 (4x), SA18, TPU, and hybrids IIUM-F1 and UiTM-H2) were evaluated for the agronomic traits under two conditions: sun light (<12 hours) and simulated light (>14 hours) using a factorial experiment. The agronomic performance of Stevia rebaudiana was significantly in long day length (>14 hours) environment comparing with short day length (<12 hours) environment. Stevia plants under sun light start to flower after seven weeks, from the other hand stevia plants under simulated light did not flower. All stevia genotypes showed a high performance under long day length (>14 hours) environments.

The heading-date gene Ghd7 inhibits seed germination by modulating the balance between abscisic acid and gibberellins

Seed dormancy of cultivated rice was largely weakened during the progress of domestication.Correct timing and uniformity of seed germination are important for rapid seedling establishment and highyield production.In the present study,we found that the heading-date gene Ghd7 acted as a negative regulator of germination.A mutant of ghd7 showed low sensitivity to exogenous ABA treatment during seed germination.Further investigation revealed reduced accumulation of ABA in mature ghd7 seeds as a consequence of dampened expression of OsNCED genes.Moreover,elevated GA_(3) level was detected in seeds of ghd7 mutant during imbibition course,which was attributed to the induction of genes responsible for the synthesis pathways of bioactive GAs.Thus,Ghd7 inhibits seed germination by increasing the ABA/GA_(3) ratio.Besides revealing pleiotropic effects of Ghd7,our results indicate its role in linking seed germination to growth-phase transition in rice,which would enrich the theoretical basis for future breeding practices.

Genomic Survey and Expression Profiling of the MYB Gene Family in Watermelon

Myeloblastosis(MYB)proteins constitute one of the largest transcription factor(TF)families in plants.They are functionally diverse in regulating plant development,metabolism,and multiple stress responses.However,the function of watermelon MYB proteins remains elusive to date.Here,a genome-wide identification of watermelon MYB TFs was performed by bioinformatics analysis.A total of 162 MYB genes were identified from watermelon(Cla MYB).A comprehensive overview of the Cla MYB genes was undertaken,including the gene structures,chromosomal distribution,gene duplication,conserved protein motif,and phylogenetic relationship.According to the analyses,the watermelon MYB genes were categorized into three groups(R1R2R3-MYB,R2R3-MYB,and MYB-related).Amino acid alignments for all MYB motifs of Cla MYBs demonstrated high conservation.Investigation of their chromosomal localization revealed that these Cla MYB genes distributed across the 11watermelon chromosomes.Gene duplication analyses showed that tandem duplication events contributed predominantly to the expansion of the MYB gene family in the watermelon genome.Phylogenetic comparison of the Cla MYB proteins with Arabidopsis MYB proteins revealed that watermelon MYB proteins underwent a more diverse evolution after divergence from Arabidopsis.Some watermelon MYBs were found to cluster into the functional clades of Arabidopsis MYB proteins.Expression analysis under different stress conditions identified a group of watermelon MYB proteins implicated in the plant stress responses.The comprehensive investigation of watermelon MYB genes in this study provides a useful reference for future cloning and functional analysis of watermelon MYB proteins.