Person: Zhuanfang Hao
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Zhuanfang Hao
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Zhuanfang Hao
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- ZmADF5, a maize actin-depolymerizing factor conferring enhanced drought tolerance in maize(MDPI, 2024) Bojuan Liu; Nan Wang; Ruisi Yang; Xiaonan Wang; Ping Luo; Yong Chen; Fei Wang; Mingshun Li; Jianfeng Weng; Degui Zhang; Hongjun Yong; Jienan Han; Zhiqiang Zhou; Xuecai Zhang; Zhuanfang Hao; Xinhai Li
Publication - Genomic prediction of yield performance among single-cross maize hybrids using a partial diallel cross design(Institute of Crop Sciences, 2023) Ping Luo; Houwen Wang; Zhiyong Ni; Ruisi Yang; Fei Wang; Hongjun Yong; Lin Zhang; Zhiqiang Zhou; Wei Song; Mingshun Li; Jie Yang; Jianfeng Weng; Zhaodong Meng; Degui Zhang; Jienan Han; Yong Chen; Runze Zhang; Liwei Wang; Meng Zhao; Wenwei Gao; Xiaoyu Chen; Wenjie Li; Zhuanfang Hao; Junjie Fu; Xuecai Zhang; Xinhai Li
Publication - Natural variations in the non-coding region of ZmNAC080308 contributes maintaining grain yield under drought stress in maize(BioMed Central, 2021) Nan Wang; Cheng, Ming; Yong Chen; Bojuan Liu; Xiaonan Wang; Guojun Li; Yueheng Zhou; Ping Luo; Zhangying Xi; Hongjun Yong; Degui Zhang; Mingshun Li; Xuecai Zhang; San Vicente Garcia, F.M.; Zhuanfang Hao; Xinhai Li
Publication - Genomic prediction across years in a maize doubled haploid breeding program to accelerate early-stage testcross testing(Springer, 2020) Nan Wang; Hui Wang; Ao Zhang; Yubo Liu; Diansi Yu; Zhuanfang Hao; Ilut, D.; Glaubitz, J.C.; Yanxin Gao; Jones, E.; Olsen, M.; Xinhai Li; San Vicente Garcia, F.M.; Prasanna, B.M.; Crossa, J.; Pérez-Rodríguez, P.; Xuecai Zhang
Publication - Applications of genotyping-by-sequencing (GBS) in maize genetics and breeding(Nature Publishing Group, 2020) Nan Wang; Yibing Yuan; Hui Wang; Diansi Yu; Yubo Liu; Ao Zhang; Gowda, M.; Nair, S.K.; Zhuanfang Hao; Yanli Lu; San Vicente Garcia, F.M.; Prasanna, B.M.; Xinhai Li; Xuecai Zhang
Publication - Genome-wide association mapping and genomic prediction analyses reveal the genetic architecture of grain yield and flowering time under drought and heat stress conditions in maize(Blackwell Verlag, 2019) Yibing Yuan; Cairns, J.E.; Babu, R.; Gowda, M.; Makumbi, D.; Magorokosho, C.; Ao Zhang; Yubo Liu; Nan Wang; Zhuanfang Hao; San Vicente Garcia, F.M.; Olsen, M.; Prasanna, B.M.; Yanli Lu; Xuecai ZhangDrought stress (DS) is a major constraint to maize yield production. Heat stress (HS) alone and in combination with DS are likely to become the increasing constraints. Association mapping and genomic prediction (GP) analyses were conducted in a collection of 300 tropical and subtropical maize inbred lines to reveal the genetic architecture of grain yield and flowering time under well-watered (WW), DS, HS, and combined DS and HS conditions. Out of the 381,165 genotyping-by-sequencing SNPs, 1549 SNPs were significantly associated with all the 12 trait-environment combinations, the average PVE (phenotypic variation explained) by these SNPs was 4.33%, and 541 of them had a PVE value greater than 5%. These significant associations were clustered into 446 genomic regions with a window size of 20 Mb per region, and 673 candidate genes containing the significantly associated SNPs were identified. In addition, 33 hotspots were identified for 12 trait-environment combinations and most were located on chromosomes 1 and 8. Compared with single SNP-based association mapping, the haplotype-based associated mapping detected fewer number of significant associations and candidate genes with higher PVE values. All the 688 candidate genes were enriched into 15 gene ontology terms, and 46 candidate genes showed significant differential expression under the WW and DS conditions. Association mapping results identified few overlapped significant markers and candidate genes for the same traits evaluated under different managements, indicating the genetic divergence between the individual stress tolerance and the combined drought and HS tolerance. The GP accuracies obtained from the marker-trait associated SNPs were relatively higher than those obtained from the genome-wide SNPs for most of the target traits. The genetic architecture information of the grain yield and flowering time revealed in this study, and the genomic regions identified for the different trait-environment combinations are useful in accelerating the efforts on rapid development of the stress-tolerant maize germplasm through marker-assisted selection and/or genomic selection.
Publication - Zea mays (L.) P1 locus for cob glume color identified as a post-domestication selection target with an effect on temperate maize genomes(Elsevier, 2013) Chuanxiao Xie; Jianfeng Weng; Wenguo Liu; Cheng Zou; Zhuanfang Hao; Wenxue Li; Minshun Li; Xiaosen Guo; Gengyun Zhang; Yunbi Xu; Xinhai Li; Shihuang ZhangArtificial selection during domestication and post-domestication improvement results in loss of genetic diversity near target loci. However, the genetic locus associated with cob glume color and the nature of the genomic pattern surrounding it was elusive and the selection effect in that region was not clear. An association mapping panel consisting of 283 diverse modern temperate maize elite lines was genotyped by a chip containing over 55,000 evenly distributed SNPs. Ten-fold resequencing at the target region on 40 of the panel lines and 47 tropical lines was also undertaken. A genome-wide association study (GWAS) for cob glume color confirmed the P1 locus, which is located on the short arm of chromosome 1, with a ; log10P value for surrounding SNPs higher than the Bonferroni threshold ( < 0.001) when a mixed linear model (MLM) was implemented. A total of 26 markers were identified in a 0.78 Mb region surrounding the P1 locus, including 0.73 Mb and 0.05 Mb upstream and downstream of the P1 gene, respectively. A clear linkage disequilibrium (LD) block was found and LD decayed very rapidly with increasing physical distance surrounding the P1 locus. The estimates of ; and Tajima's D were significantly (P < 0.001) lower at both ends compared to the locus. Upon comparison of temperate and tropical lines at much finer resolution by resequencing (180-fold finer than chip SNPs), a more structured LD block pattern was found among the 40 resequenced temperate lines. All evidence indicates that the P1 locus in temperate maize has not undergone neutral evolution but has been subjected to artificial selection during post-domestication selection or improvement. The information and analytical results generated in this study provide insights as to how breeding efforts have affected genome evolution in crop plants.
Publication - Revisiting the hetero-fertilization phenomenon in maize(Public Library of Science, 2011) Shibin Gao; Babu, R.; Yanli Lu; Martínez, C.A.; Zhuanfang Hao; Krivanek, A.F.; Jiankang Wang; Tingzhao Rong; Crouch, J.H.; Yunbi XuDevelopment of a seed DNA-based genotyping system for marker-assisted selection (MAS) has provided a novel opportunity for understanding aberrant reproductive phenomena such as hetero-fertilization (HF) by observing the mismatch of endosperm and leaf genotypes in monocot species. In contrast to conventional approaches using specific morphological markers, this approach can be used for any population derived from diverse parental genotypes. A large-scale experiment was implemented using seven F2 populations and four three-way cross populations, each with 534 to 1024 individuals. The frequency of HF within these populations ranged from 0.14% to 3.12%, with an average of 1.46%. The highest frequency of HF in both types of population was contributed by the pollen gametes. Using three-way crosses allowed, for the first time, detection of the HF contributed by maternal gametes, albeit at very low frequency (0.14%?0.65%). Four HF events identified from each of two F2 populations were tested and confirmed using 1032 single nucleotide polymorphic markers. This analysis indicated that only 50% of polymorphic markers can detect a known HF event, and thus the real HF frequency can be inferred by doubling the estimate obtained from using only one polymorphic marker. As expected, 99% of the HF events can be detected by using seven independent markers in combination. Although seed DNA-based analysis may wrongly predict plant genotypes due to the mismatch of endosperm and leaf DNA caused by HF, the relatively low HF frequencies revealed with diverse germplasm in this study indicates that the effect on the accuracy of MAS is limited. In addition, comparative endosperm and leaf DNA analysis of specific genetic stocks could be useful for revealing the relationships among various aberrant fertilization phenomena including haploidy and apomixis.
Publication - 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 XuUnderstanding 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.
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