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Jing Wang

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Jing Wang
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Jing Wang
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    Identification of candidate genes for drought tolerance by whole-genome resequencing in maize
    (Springer Nature, 2014) Jie Xu; Yuan, Y.; Yunbi Xu; Gengyun Zhang; Guo, X.; Wu, F.; Wang, Q; Tingzhao Rong; Pan, G.; Cao, M.; Tang, Q.; Shibin Gao; Yaxi Liu; Jing Wang; Hai Lan; Lu, Y.
    Drought stress is one of the major limiting factors for maize production. With the availability of maize B73 reference genome and whole-genome resequencing of 15 maize inbreds, common variants (CV) and clustering analyses were applied to identify non-synonymous SNPs (nsSNPs) and corresponding candidate genes for drought tolerance. A total of 524 nsSNPs that were associated with 271 candidate genes involved in plant hormone regulation, carbohydrate and sugar metabolism, signaling molecules regulation, redox reaction and acclimation of photosynthesis to environment were detected by CV and cluster analyses. Most of the nsSNPs identified were clustered in bin 1.07 region that harbored six previously reported QTL with relatively high phenotypic variation explained for drought tolerance. Genes Ontology (GO) analysis of candidate genes revealed that there were 35 GO terms related to biotic stimulus and membrane-bounded organelle, showing significant differences between the candidate genes and the reference B73 background. Changes of expression level in these candidate genes for drought tolerance were detected using RNA sequencing for fertilized ovary, basal leaf meristem tissue and roots collected under drought stressed and well-watered conditions. The results indicated that 70% of candidate genes showed significantly expression changes under two water treatments and our strategies for mining candidate genes are feasible and relatively efficient. Our results successfully revealed candidate nsSNPs and associated genes for drought tolerance by comparative sequence analysis of 16 maize inbred lines. Both methods we applied were proved to be efficient for identifying candidate genes for complex traits through the next-generation sequencing technologies (NGS). These selected genes will not only facilitate understanding of genetic basis of drought stress response, but also accelerate genetic improvement through marker-assisted selection in maize.
    Publication
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    Evaluation of the APSIM model in cropping systems of Asia
    (Elsevier, 2017) Gaydon, D.; Singh, B.; Wang, E.; Poulton, P.L.; Ahmad, B.; Ahmed, F.; Akhter, S.; Ali, I.; Amarasingha, R.; Chaki, A.K.; Chen, C.; Choudhury, B.U.; Darai, R.; Das, A.; Hochman, Z.; Horan, H.; Hosang, E.Y.; Vijaya Kumar, P.; Khan, A.S.M.M.R.; Laing, Alison; Liu, L.; Malaviachichi, M.A.P.W.K; Mohapatra, K.P.; Muttaleb, M.A.; Power, B.; Radanielson, A.; Rai, G.S.; Rashid, M.H.; Rathanayake, W.M.U.K.; Sarker, M.M.R.; Sena, D.R.; Shamim, M.; Subash, N.; Suriadi, A.; Suriyagoda, L.D.B.; Wang, G.; Jing Wang; Yadav, R.K.; Roth, C.H.
    Resource shortages, driven by climatic, institutional and social changes in many regions of Asia, combined with growing imperatives to increase food production whilst ensuring environmental sustainability, are driving research into modified agricultural practices. Well-tested cropping systems models that capture interactions between soil water and nutrient dynamics, crop growth, climate and farmer management can assist in the evaluation of such new agricultural practices. One such cropping systems model is the Agricultural Production Systems Simulator (APSIM). We evaluated APSIM’s ability to simulate the performance of cropping systems in Asia from several perspectives: crop phenology, production, water use, soil dynamics (water and organic carbon) and crop CO2 response, as well as its ability to simulate cropping sequences without reset of soil variables. The evaluation was conducted over a diverse range of environments (12 countries, numerous soils), crops and management practices throughout the region. APSIM’s performance was statistically assessed against assembled replicated experimental datasets. Once properly parameterised, the model performed well in simulating the diversity of cropping systems to which it was applied with RMSEs generally less than observed experimental standard deviations (indicating robust model performance), and with particular strength in simulation of multi-crop sequences. Input parameter estimation challenges were encountered, and although ‘work-arounds’ were developed and described, in some cases these actually represent model deficiencies which need to be addressed. Desirable future improvements have been identified to better position APSIM as a useful tool for Asian cropping systems research into the future. These include aspects related to harsh environments (high temperatures, diffuse light conditions, salinity, and submergence), conservation agriculture, greenhouse gas emissions, as well as aspects more specific to Southern Asia and low input systems (such as deficiencies in soil micro-nutrients).
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    Development and characterization of simple sequence repeat markers providing genome-wide coverage and high resolution in maize
    (Oxford University Press, 2013) Jie Xu; Ling Liu; Yunbi Xu; Churun Chen; Tingzhao Rong; Farhan Ali; Shufeng Zhou; Fengkai Wu; Yaxi Liu; Jing Wang; Moju Cao; Yanli Lu
    Simple sequence repeats (SSRs) have been widely used in maize genetics and breeding, because they are co-dominant, easy to score, and highly abundant. In this study, we used whole-genome sequences from 16 maize inbreds and 1 wild relative to determine SSR abundance and to develop a set of high-density polymorphic SSR markers. A total of 264 658 SSRs were identified across the 17 genomes, with an average of 135 693 SSRs per genome. Marker density was one SSR every of 15.48 kb. (C/G)n, (AT)n, (CAG/CTG)n, and (AAAT/ATTT)n were the most frequent motifs for mono, di-, tri-, and tetra-nucleotide SSRs, respectively. SSRs were most abundant in intergenic region and least frequent in untranslated regions, as revealed by comparing SSR distributions of three representative resequenced genomes. Comparing SSR sequences and e-polymerase chain reaction analysis among the 17 tested genomes created a new database, including 111 887 SSRs, that could be develop as polymorphic markers in silico. Among these markers, 58.00, 26.09, 7.20, 3.00, 3.93, and 1.78% of them had mono, di-, tri-, tetra-, penta-, and hexa-nucleotide motifs, respectively. Polymorphic information content for 35 573 polymorphic SSRs out of 111 887 loci varied from 0.05 to 0.83, with an average of 0.31 in the 17 tested genomes. Experimental validation of polymorphic SSR markers showed that over 70% of the primer pairs could generate the target bands with length polymorphism, and these markers would be very powerful when they are used for genetic populations derived from various types of maize germplasms that were sampled for this study.
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    Comparative SNP and haplotype analysis reveals a higher genetic diversity and rapider LD decay in tropical than temperate germplasm in maize
    (Public Library of Science, 2011) Yanli Lu; Shah, T.; Zhuanfang Hao; Taba, S.; Shihuang Zhang; Shibin Gao; Jian Liu; Moju Cao; Jing Wang; A. Bhanu Prakash; Tingzhao Rong; Yunbi Xu
    Understanding of genetic diversity and linkage disequilibrium (LD) decay in diverse maize germplasm is fundamentally important for maize improvement. A total of 287 tropical and 160 temperate inbred lines were genotyped with 1943 single nucleotide polymorphism (SNP) markers of high quality and compared for genetic diversity and LD decay using the SNPs and their haplotypes developed from genic and intergenic regions. Intronic SNPs revealed a substantial higher variation than exonic SNPs. The big window size haplotypes (3-SNP slide-window covering 2160 kb on average) revealed much higher genetic diversity than the 10 kb-window and gene-window haplotypes. The polymorphic information content values revealed by the haplotypes (0.436?0.566) were generally much higher than individual SNPs (0.247?0.259). Cluster analysis classified the 447 maize lines into two major groups, corresponding to temperate and tropical types. The level of genetic diversity and subpopulation structure were associated with the germplasm origin and post-domestication selection. Compared to temperate lines, the tropical lines had a much higher level of genetic diversity with no significant subpopulation structure identified. Significant variation in LD decay distance (2?100 kb) was found across the genome, chromosomal regions and germplasm groups. The average of LD decay distance (10?100 kb) in the temperate germplasm was two to ten times larger than that in the tropical germplasm (5?10 kb). In conclusion, tropical maize not only host high genetic diversity that can be exploited for future plant breeding, but also show rapid LD decay that provides more opportunity for selection.
    Publication