Person: Jianbing Yan
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Jianbing Yan
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Jianbing Yan
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- Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights(Nature Research, 2014) Weiwei Wen; Dong Li; Xiang Li; Yanqiang Gao; Wenqiang Li; Huihui Li; Jie Liu; Haijun Liu; Wei Chen; Jie Luo; Jianbing YanPlants produce a variety of metabolites that have a critical role in growth and development. Here we present a comprehensive study of maize metabolism, combining genetic, metabolite and expression profiling methodologies to dissect the genetic basis of metabolic diversity in maize kernels. We quantify 983 metabolite features in 702 maize genotypes planted at multiple locations. We identify 1,459 significant locus–trait associations (P≤1.8 × 10−6) across three environments through metabolite-based genome-wide association mapping. Most (58.5%) of the identified loci are supported by expression QTLs, and some (14.7%) are validated through linkage mapping. Re-sequencing and candidate gene association analysis identifies potential causal variants for five candidate genes involved in metabolic traits. Two of these genes were further validated by mutant and transgenic analysis. Metabolite features associated with kernel weight could be used as biomarkers to facilitate genetic improvement of maize.
Publication - Genome-wide association mapping reveals novel sources of resistance to northern corn leaf blight in maize(BioMed Central, 2015) Junqiang Ding; Farhan Ali; Gengshen Chen; Huihui Li; Mahuku, G.; Ning Yang; Narro, L.A.; Magorokosho, C.; Makumbi, D.; Jianbing YanBackground: Northern corn leaf blight (NCLB) caused by Exserohilum turcicum is a destructive disease in maize. Using host resistance to minimize the detrimental effects of NCLB on maize productivity is the most cost-effective and appealing disease management strategy. However, this requires the identification and use of stable resistance genes that are effective across different environments. Results: We evaluated a diverse maize population comprised of 999 inbred lines across different environments for resistance to NCLB. To identify genomic regions associated with NCLB resistance in maize, a genome-wide association analysis was conducted using 56,110 single-nucleotide polymorphism markers. Single-marker and haplotype-based associations, as well as Anderson-Darling tests, identified alleles significantly associated with NCLB resistance. The single-marker and haplotype-based association mappings identified twelve and ten loci (genes), respectively, that were significantly associated with resistance to NCLB. Additionally, by dividing the population into three subgroups and performing Anderson-Darling tests, eighty one genes were detected, and twelve of them were related to plant defense. Identical defense genes were identified using the three analyses. Conclusion: An association panel including 999 diverse lines was evaluated for resistance to NCLB in multiple environments, and a large number of resistant lines were identified and can be used as reliable resistance resource in maize breeding program. Genome-wide association study reveals that NCLB resistance is a complex trait which is under the control of many minor genes with relatively low effects. Pyramiding these genes in the same background is likely to result in stable resistance to NCLB.
Publication - Comparative analysis of carotenoid and tocopherol compositions in high-oil and normal maize (Zea mays L.) inbreds(Institute of Crop Sciences, 2009) Zhou, Yi; Zhiyuan Fu; Qing Li; Xu Shu-Tu; Chander, S.; XiaoHong Yang; Jiansheng Li; Jianbing YanAmong staple crops, maize has a high amount of carotenoids and tocopherols, which have a number of beneficial effects on human health. The former is the main dietary precursor of vitamin A. The latter is an essential macronutrient which acts as antioxidant shows the benefit in the prevention of certain types of diseases for human. In this study, high performance liquid chromatography (HPLC) was developed and used for simultaneously measuring the contents of carotenoids and tocopherols in maize grain for 112 yellow-endosperm inbred lines, including 32 high-oil lines and 80 normal lines widely used in Chinese breeding programs. Broad phenotypic diversity was observed for all measured traits. Among the eight components analyzed, a-tocopherol showed the largest variation with 162 times content difference while -tocopherol showed the smallest variation with four times content difference. The tocopherol content in high-oil maize lines was significantly higher than that in normal lines. However, the carotenoids content in high-oil lines showed no significant differences from that in normal lines, which had wider phenotypic variations. The mean values of y-tocopherol, a-tocopherol, and total tocopherol contents in high-oil lines were 2.4, 2.5, and 2.4 times higher than those in normal lines. Compared with normal lines, the high-oil lines contained broader genetic variations for some tocopherols though the number of high-oil lines (32) was far smaller than that of normal lines (80). All the present results provided some beneficial informations for future breeding at the target of three-high nutritional maize: high-oil, high provitamin A, and high vitamin E.
Publication - Quantitative trait loci mapping for adult-plant resistance to powdery mildew in Chinese wheat cultivar Bainong 64(American Phytopathological Society (APS), 2009) Lan, C.; Shanshan Liang; Wang, Z.L.; Jianbing Yan; Yong Zhang; Xianchun Xia; He ZhonghuAdult-plant resistance (APR) is an effective means of controlling powdery mildew in wheat. In the present study, 406 simple-sequence repeat markers were used to map quantitative trait loci (QTLs) for APR to powdery mildew in a doubled-haploid (DH) population of 181 lines derived from the cross Bainong 64 × Jingshuang 16. The DH lines were planted in a randomized complete block design with three replicates in Beijing and Anyang during the 2005?06 and 2007?08 cropping seasons. Artificial inoculations were carried out in Beijing using the highly virulent Blumeria graminis f. sp. tritici isolate E20. Disease severities on penultimate leaves were scored twice in Beijing whereas, at Anyang, maximum disease severities (MDS) were recorded following natural infection. Broad-sense heritabilities of MDS and areas under the disease progress curve were 0.89 and 0.77, respectively, based on the mean values averaged across environments. Composite interval mapping detected four QTLs for APR to powdery mildew on chromosomes 1A, 4DL, 6BS, and 7A; these were designated QPm.caas-1A, QPm.caas-4DL, QPm.caas-6BS, and QPm.caas-7A, respectively, and explained 6.3 to 22.7% of the phenotypic variance. QTLs QPm.caas-4DL and QPm.caas-6BS were stable across environments with high genetic effects on powdery mildew response, accounting for 15.2 to 22.7% and 9.0 to 13.2% of the phenotypic variance, respectively. These results should be useful for the future improvement of powdery mildew resistance in wheat.
Publication - Validation of the effects of molecular marker polymorphisms in LcyE and CrtRB1 on provitamin A concentrations for 26 tropical maize populations(Springer, 2012) Babu, R.; Palacios-Rojas, N.; Shibin Gao; Jianbing Yan; Pixley, K.V.Vitamin A deficiency (VAD) compromises immune function and is the leading cause of preventable blindness in children in many developing countries. Biofortification, or breeding staple food crops that are rich in micronutrients, provides a sustainable way to fight VAD and other micronutrient malnutrition problems. Polymorphisms, with associated molecular markers, have recently been identified for two loci, LcyE (lycopene epsilon cyclase) and CrtRB1 (¦Â-carotene hydroxylase 1) that govern critical steps in the carotenoid biosynthetic pathway in maize endosperm, thereby enabling the opportunity to integrate marker-assisted selection (MAS) into carotenoid breeding programs. We validated the effects of 3 polymorphisms (LcyE5¡äTE, LcyE3¡äIndel and CrtRB1-3¡äTE) in 26 diverse tropical genetic backgrounds. CrtRB1-3¡äTE had a two-ten fold effect on enhancing beta-carotene (BC) and total provitamin A (proA) content. Reduced-function, favorable polymorphisms within LcyE resulted in 0¨C30 % reduction in the ratio of alpha- to beta-branch carotenoids, and increase in proA content (sometimes statistically significant). CrtRB1-3¡äTE had large, significant effect on enhancing BC and total ProA content, irrespective of genetic constitution for LcyE5¡äTE. Genotypes with homozygous favorable CrtRB1-3¡äTE alleles had much less zeaxanthin and an average of 25 % less total carotenoid than other genotypes, suggesting that feedback inhibition may be reducing the total flux into the carotenoid pathway. Because this feedback inhibition was most pronounced in the homozygous favorable LcyE (reduced-function) genotypes, and because maximum total proA concentrations were achieved in genotypes with homozygous unfavorable or heterozygous LcyE, we recommend not selecting for both reduced-function genes in breeding programs. LcyE exhibited significant segregation distortion (SD) in all the eight, while CrtRB1 in five of eight digenic populations studied, with favorable alleles of both the genes frequently under-represented. MAS using markers reported herein can efficiently increase proA carotenoid concentration in maize.
Publication - Genetic characterization of a core set of a tropical maize race Tuxpeño for further use in maize improvement(Public Library of Science, 2012) Weiwei Wen; Franco, J.; Chavez Tovar, V.H.; Jianbing Yan; Taba, S.The tropical maize race Tuxpeño is a well-known race of Mexican dent germplasm which has greatly contributed to the development of tropical and subtropical maize gene pools. In order to investigate how it could be exploited in future maize improvement, a panel of maize germplasm accessions was assembled and characterized using genome-wide Single Nucleotide Polymorphism (SNP) markers. This panel included 321 core accessions of Tuxpeño race from the International Maize and Wheat Improvement Center (CIMMYT) germplasm bank collection, 94 CIMMYT maize lines (CMLs) and 54 U.S. Germplasm Enhancement of Maize (GEM) lines. The panel also included other diverse sources of reference germplasm: 14 U.S. maize landrace accessions, 4 temperate inbred lines from the U.S. and China, and 11 CIMMYT populations (a total of 498 entries with 795 plants). Clustering analyses (CA) based on Modified Rogers Distance (MRD) clearly partitioned all 498 entries into their corresponding groups. No sub clusters were observed within the Tuxpeño core set. Various breeding strategies for using the Tuxpeño core set, based on grouping of the studied germplasm and genetic distance among them, were discussed. In order to facilitate sampling diversity within the Tuxpeño core, a minicore subset of 64 Tuxpeño accessions (20% of its usual size) representing the diversity of the core set was developed, using an approach combining phenotypic and molecular data. Untapped diversity represents further use of the Tuxpeño landrace for maize improvement through the core and/or minicore subset available to the maize community.
Publication - An 11-bp insertion in Zea mays fatb reduces the palmitic acid content of fatty acids in Maize grain(Public Library of Science, 2011) Lin Li; Hui Li; Qing Li; Yang XiaoHong; Debo Zheng; Warburton, M.; Yuchao Chai; Pan Zhang; Yuqiu Guo; Jianbing Yan; Jiansheng LiThe ratio of saturated to unsaturated fatty acids in maize kernels strongly impacts human and livestock health, but is a complex trait that is difficult to select based on phenotype. Map-based cloning of quantitative trait loci (QTL) is a powerful but time-consuming method for the dissection of complex traits. Here, we combine linkage and association analyses to fine map QTL-Pal9, a QTL influencing levels of palmitic acid, an important class of saturated fatty acid. QTL-Pal9 was mapped to a 90-kb region, in which we identified a candidate gene, Zea mays fatb (Zmfatb), which encodes acyl-ACP thioesterase. An 11-bp insertion in the last exon of Zmfatb decreases palmitic acid content and concentration, leading to an optimization of the ratio of saturated to unsaturated fatty acids while having no effect on total oil content. We used three-dimensional structure analysis to explain the functional mechanism of the ZmFATB protein and confirmed the proposed model in vitro and in vivo. We measured the genetic effect of the functional site in 15 different genetic backgrounds and found a maximum change of 4.57 mg/g palmitic acid content, which accounts for ~20?60% of the variation in the ratio of saturated to unsaturated fatty acids. A PCR-based marker for QTL-Pal9 was developed for marker-assisted selection of nutritionally healthier maize lines. The method presented here provides a new, efficient way to clone QTL, and the cloned palmitic acid QTL sheds lights on the genetic mechanism of oil biosynthesis and targeted maize molecular breeding.
Publication - Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought(Oxford University Press, 2011) Setter, T.; Jianbing Yan; Warburton, M.; Ribaut, J.M.; Yunbi Xu; Sawkins, M.C.; Buckler, E.; Zhiwu Zhang; Gore, M.A.In maize, water stress at flowering causes loss of kernel set and productivity. While changes in the levels of sugars and abscisic acid (ABA) are thought to play a role in this stress response, the mechanistic basis and genes involved are not known. A candidate gene approach was used with association mapping to identify loci involved in accumulation of carbohydrates and ABA metabolites during stress. A panel of single nucleotide polymorphisms (SNPs) in genes from these metabolic pathways and in genes for reproductive development and stress response was used to genotype 350 tropical and subtropical maize inbred lines that were well watered or water stressed at flowering. Pre-pollination ears, silks, and leaves were analysed for sugars, starch, proline, ABA, ABA-glucose ester, and phaseic acid. ABA and sugar levels in silks and ears were negatively correlated with their growth. Association mapping with 1229 SNPs in 540 candidate genes identified an SNP in the maize homologue of the Arabidopsis MADS-box gene, PISTILLATA, which was significantly associated with phaseic acid in ears of well-watered plants, and an SNP in pyruvate dehydrogenase kinase, a key regulator of carbon flux into respiration, that was associated with silk sugar concentration. An SNP in an aldehyde oxidase gene was significantly associated with ABA levels in silks of water-stressed plants. Given the short range over which decay of linkage disequilibrium occurs in maize, the results indicate that allelic variation in these genes affects ABA and carbohydrate metabolism in floral tissues during drought.
Publication - Relationship, evolutionary fate and function of two maize co-orthologs of rice GW2 associated with kernel size and weight(BioMed Central, 2010) Qing Li; Lin Li; XiaoHong Yang; Warburton, M.; Bai Guanghong; Dai JingRui; Jiansheng Li; Jianbing YanBackground: In rice, the GW2 gene, found on chromosome 2, controls grain width and weight. Two homologs of this gene, ZmGW2-CHR4 and ZmGW2-CHR5, have been found in maize. In this study, we investigated the relationship, evolutionary fate and putative function of these two maize genes. Results: The two genes are located on duplicated maize chromosomal regions that show co-orthologous relationships with the rice region containing GW2. ZmGW2-CHR5 is more closely related to the sorghum counterpart than to ZmGW2-CHR4. Sequence comparisons between the two genes in eight diverse maize inbred lines revealed that the functional protein domain of both genes is completely conserved, with no nonsynonymous polymorphisms identified. This suggests that both genes may have conserved functions, a hypothesis that was further confirmed through linkage, association, and expression analyses. Linkage analysis showed that ZmGW2-CHR4 is located within a consistent quantitative trait locus (QTL) for one-hundred kernel weight (HKW). Association analysis with a diverse panel of 121 maize inbred lines identified one single nucleotide polymorphism (SNP) in the promoter region of ZmGW2-CHR4 that was significantly associated with kernel width (KW) and HKW across all three field experiments examined in this study. SNPs or insertion/deletion polymorphisms (InDels) in other regions of ZmGW2-CHR4 and ZmGW2-CHR5 were also found to be significantly associated with at least one of the four yield-related traits (kernel length (KL), kernel thickness (KT), KW and HKW). None of the polymorphisms in either maize gene are similar to each other or to the 1 bp InDel causing phenotypic variation in rice. Expression levels of both maize genes vary over ear and kernel developmental stages, and the expression level of ZmGW2- CHR4 is significantly negatively correlated with KW.
Publication - Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers(Public Library of Science, 2009) Jianbing Yan; Shah, T.; Warburton, M.; Buckler, E.; McMullen, M.D.; Crouch, J.H.A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by geographic origin, and subgroups of different sample sizes. The LD decay distance differed among chromosomes and ranged between 1 to 10 kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core set of inbreds was defined based on haplotypes, and 60 lines capture 90% of the haplotype diversity of the entire panel. The defined core sets and the entire collection can be used widely for different research targets.
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