Xin-Hai Li

Comparative QTL Mapping of Resistance to Gray Leaf Spot in Maize Based on Bioinformatics

The integration QTL map for gray leaf spot resistance in maize was constructed by compiling a total of 57 QTLs available with genetic map IBM2 2005 neighbors as reference. Twenty-six ”real QTLs” and seven consensus QTLs were identified by refining these 57 QTLs using overview and meta-analysis approaches. Seven consensus QTLs were found on chromosomes 1.06, 2.06, 3.04, 4.06, 4.08, 5.03, and 8.06, and the map coordinates were 552.53, 425.72, 279.20, 368.97, 583.21, 308.68 and 446.14 cM, respectively. Using a synteny conservation approach based on comparative mapping between the maize genetic map and rice physical map, a total of 69 rice and maize resistance genes collected from websites Gramene and MaizeGDB were projected onto the maize genetic map IBM2 2005 neighbors, and 2 (Rgene32, ht1), 4 (Rgene5, rp3, scmv2, wsm2), and 4 (ht2, Rgene6, Rgene8 and Rgene7) positional candidate genes were found in three consensus QTLs on chromosomes 2.06, 3.04, and 8.06, respectively. The results suggested that the combination of meta-analysis of gray leaf spot in maize and sequence homologous comparison between maize and rice could be an efficient strategy for identifying major QTLs and corresponding candidate genes for the gray leaf spot.

Analysis of Meta-QTL and Candidate Genes Related to Yield Components in Maize

In this study, 584 QTLs related to grain yield components (row number, kernel number per row and kernel weight) in maize were integrated from the published papers between 1994 and 2012 using the reference map of IBM2 2008 Neighbors high density maize genetic map. By Meta-analysis method, 73 Meta-QTLs for grain yield components were estimated, including 22 QTLs for row number, 7 QTLs for kernel number per row and 44 QTLs for kernel weight. With the B73 genome sequences, 10 maize genes and 12 rice homologous candidate genes related to yield components were comparatively and electronically mapped in consensus map, and these genes are located in maize chromosome Bins 1.04, 1.06, 1.07, 2.04, 2.06, 3.04, 4.05, 4.07, 4.09, 5.03, 5.04, 5.05, 7.02, 8.03, 9.03, 10.06, and 10.07. The analysis of Meta-QTL and candidate genes related to grain yield components will provide useful information for marker-assisted selection breeding and gene cloning in maize.

Identification and Mapping of a Novel Sugarcane Mosaic Virus Resistance Gene in Maize

Abstract Sugarcane mosaic virus (SCMV) causes considerable damage to maize (Zea mays L.) in China. Characterization of resistance gene(s) serves as the basis for effective selection in resistance breeding programs. The objective of this study was to identify novel genes conferring resistance to SCMV from maize germplasm in China. A total of 21 BC2F3 populations derived from 8 maize intercross combinations were artificially inoculated with SCMV under field conditions. The numbers of resistant and susceptible plants in the BC2F3 population Ye 478 × Hai 9-21 were consistent with the theoretical 1:3 phenotypic ratio, suggesting that a recessive gene derived from the resistant parent Hai 9-21 was responsible for resistance to SCMV. Bulked segregant analysis (BSA) and simple sequence repeat (SSR) marker analysis were used to verify the recessive resistance gene that was designated scm3. Gene scm3 was located in bin 3.04–3.05, flanked by SSR markers umc1965 and bnlg420 with genetic distances of 45.7 and 6.5 cM, respectively. Four additional linked markers were detected, which were associated with scm3 gene in the order of umc1965–scm3–bnlg420–umc1307–umc2265–bnlg2241–umc2166.

Development of Sequence Characterized Amplified Region (SCAR) Primers for the Detection of Resistance to Sporisorium reiliana in Maize

Abstract Head smut of maize (Zea mays L.), which was caused by Sporisorium reiliana, occurred in most of the maize growing areas of the world. The purpose of this study was to develop SCAR markers for map-based cloning of resistance genes and MAS. Two sets of BC3 progenies, one (BC3Q) derived from the cross Qi319 (resistance) × Huangzao 4 (susceptible), the other (BC3M) from Mo17 (resistance) × Huangzao 4 (susceptible), were generated. Huangzao 4 was the recurrent parent in both progenies. A combination of BSA (bulked segregant analysis) with AFLP (amplified fragment length polymorphism) method was applied to map the genes involving the resistance to S. reiliana, and corresponding resistant and susceptible bulks and their parental lines were used for screening polymorphic AFLP primer pairs. One fragment of P13M61–152 was converted into SCAR (sequence charactered amplified fragment) marker S130. The marker was mapped at chromosome bin 2.09, the interval of a major QTL region previously reported to contribute to S. reiliana resistance. Furthermore, S130 was highly associated with resistance to S. reiliana, and could be useful for marker-assisted selection and facilitate map-based cloning of resistance genes.

Analysis on breeding potential of eight synthetic populations to improve a Chinese maize hybrid Zhengdan 958: Analysis on breeding potential of eight synthetic populations to improve a Chinese maize hybrid Zhengdan 958

Maize (Zea mays L.) populations are potential sources of favorable alleles absent in parental inbred lines to improve elite hybrids. The maize hybrid Zhengdan 958 has been hampered by the lack of favorable new alleles for improving yield and commodity quality. In the present study, 16 testcrosses made by using eight synthetic populations as the donors and the two parental lines of Zhengdan 958 as the receptors were evaluated in 2009 and 2010 at Shunyi, Beijing and Xinxiang, Henan Province for grain yield and test weight. Four genetic parameters were used to determine the breeding potential of eight synthetic populations as the donors to improve the target hybrid. Several synthetic populations were identified as the potential sources of favorable alleles absent in the target hybrid for each trait evaluated. The two most promising germplasms, WBMC-4 and Shanxi Syn3, had the potential for simultaneously improving grain yield and test weight of the target hybrid, which could be used to improve the parental lines Zheng 58 and Chang 7-2, respectively, and further broaden the germplasm base of Chinese heterotic groups PA and Sipingtou.

Genomic DNA Sequence, Gene Structure, Conserved Domains, and Natural Alleles of Gln1-4 Gene in Maize

Abstract Gln1-4 is one of the important members of glutamine synthetase (GS) gene family. The objectives of this study were to isolate the genomic DNA (gDNA) sequence of Gln1-4, to analyze structure, conserved domains, and natural allelic variations of the gene, and to found a basis for association analysis of the functional sites associated with nitrogen use efficiency in maize (Zea mays L.). PCR walking strategy was applied to isolate the gDNA sequence of Gln1-4 and its flanking sequences. A total of 3724 bp gDNA sequence of Gln1-4 was assembled from the maize inbred line Mo17. The full length of the coding region was 2858 bp, which comprised of 10 exons separated by 9 introns. All the 18 splicing sites were the conserved sequence of GU at the 5′ donor sites and AG at the 3′ acceptor sites. This sequence was submitted to GenBank under the accession number EU369651. Gln1-4 encodes a GS protein with the molecular weight of 39.2 kD, which was composed of 356 amino acids. The isoelectric point was 5.202. Conserved domain searching results showed that the region from exon 2 to exon 6 at amino-terminal was an ammonium-ion-binding domain, and exon 8 to exon 9 at carboxyl terminal consisted of an ATPase activity domain. Compared with Gln1-3, Gln1-4 was highly conserved in DNA sequence, amino acid sequence, gene structure, and conserved domains with a 98.31% identity of amino acid sequence. A total of 318 types of natural DNA variation at the important and target region of Gln1-4 gene were identified among 52 maize inbred lines, of which 90% was single nucleotide polymorphisms (242) and small indels (45). The analysis of the functional sites associated with nitrogen use efficiency of Gln1-4 should focus on the binding and catalyzing domains and the splicing sites.

Cloning and Expression Analysis of Heat Shock Protein Gene ZmHsp90-1 in Maize: Cloning and Expression Analysis of Heat Shock Protein Gene ZmHsp90-1 in Maize

HSP90是普遍存在于原核和真核细胞中的一种高度保守的分子伴侣。本研究从玉米中克隆了一个HSP90同源基因, 命名为 ZmHSP90-1 基因, 并对其进行了初步的序列分析。该基因cDNA序列全长2 371 bp, 开放阅读框2 094 bp, 编码697个氨基酸, 蛋白质分子量约79.98 kD。蛋白结构预测及同源比对分析表明, ZmHSP90-1 基因编码蛋白含ATPase位点和HSP90保守结构域, 并与拟南芥、水稻等多种物种的热激蛋白高度同源; 进化树分析表明 ZmHSP90-1 与拟南芥 AtHSP90.1 基因关系较近, 蛋白序列相似性达88.3%。目的蛋白亚细胞定位显示, ZmHSP90-1蛋白在细胞质中表达。实时荧光定量PCR分析表明, ZmHSP90-1 对非生物胁迫高温、高盐、ABA、低温、干旱均具有明显的应答反应。推测 ZmHSP90-1 是玉米的一个胁迫相关基因。