Haijian Zhi

Fine Mapping and Candidate Gene Analysis of Resistance Gene RSC3Q to Soybean mosaic virus in Qihuang 1

Soybean mosaic virus (SMV) disease is one of the most destructive viral diseases in soybean (Glycine max (L.) Merr.). SMV strain SC3 is the major prevalent strain in Huang-Huai and Yangtze valleys, China. The soybean cultivar Qihuang 1 is of a rich resistance spectrum and has a wide range of application in breeding programs in China. In this study, F1, F2 and F2:3 from Qihuang 1×Nannong 1138-2 were used to study inheritance and linkage mapping of the SC3 resistance gene in Qihuang 1. The secondary F2 population and near isogenic lines (NILs) derived from residual heterozygous lines (RHLs) of Qihuang 1×Nannong 1138-2 were separatively used in the fine mapping and candidate gene analysis of the resistance gene. Results indicated that a single dominant gene (designated RSC3Q) controls resistance, which was located on chromosome 13. Two genomic-simple sequence repeat (SSR) markers BARCSOYSSR_13_1114 and BARCSOYSSR_13_1136 were found flanking the two sides of the RSC3Q. The interval between the two markers was 651 kb. Quantitative real-time PCR analysis of the candidate genes showed that five genes (Glyma13g25730, 25750, 25950, 25970 and 26000) were likely involved in soybean SMV resistance. These results would have utility in cloning of RSC3Q resistance candidate gene and marker-assisted selection (MAS) in resistance breeding to SMV.

Inheritance of Resistance to Soybean Mosaic Virus Strains SC4 and SC8 in Soybean

Abstract The objective of this study was to understand the genetic and allelomorphic relationships among different soybean (Glycine max L. Merr.) cultivars with resistance to Soybean mosaic virus (SMV). Twelve resistant (R) soybean cultivars were crossed with a susceptible (S) cultivar (Nannong 1138-2, NY30, NY185, 86-4, or 8101) to determine the inheritance of resistance to SMV strain SC4 or SC8, which were predominant in the Huang-Huai-Hai Rivers Region and Yangtze Valley in China. The R parents were also crossed with each other for allelic analysis of resistance genes from different sources. The results indicated that Ji LD42, Xudou 1, and Yuejin 4 and Qihuang 1, Zhongzuo 229, and NY58 carried a dominant resistance gene for SMV strains SC4 and SC8, respectively, whereas Kefeng 1, PI 96983, Jinda 74, Fendou 56, Dabaima, and Qihuang 22 carried single dominant resistance gene for both SC4 and SC8. The allelism test of the resistance genes to SC4 showed that the resistance genes between Dabaima and Fendou 56, Kefeng 1, and Qihuang 1, between Ji LD42 and Fendou 56, and between Jinda 74 and Zhongzuo 229 were not at the same loci. The study of resistance of F2 plants and F2:3 families to SC8 indicated that the single dominant resistance genes in Jinda 74 and Fendou 56 shared a common locus or two closely loci. The resistance genes between Qihuang 1 and Kefeng 1 and between Dabaima and Fendou 56 were not at the same locus for SC8. These results are useful to understand the genetic and allelomorphic relationships among various sources of resistance.

Identification of candidate genes for resistance to Soybean mosaic virus strain SC3 by using fine mapping and transcriptome analyses

Abstract. This study is a continuation of our earlier reports on the identification and mapping of the Soybean mosaic virus (SMV) strain SC3 resistance gene present on chromosome 13 (LG F) of soybean (Glycine max (L.) Merr.). We used a combination of fine mapping and transcriptome sequencing to discover the candidate genes for SMV resistance in Qihuang-1. To fine-map the resistance gene, near-isogenic lines (NILs) from a cross between Qihuang-1 (resistant) and Nannong 1138-2 (susceptible) were genotyped with simple sequence repeats (SSR) and insertion and deletion (indel) markers to identify recombination events. Analysis of plants carrying key recombination events placed the resistance gene to a 180-kb region of the ‘Williams 82’ genome sequence with 17 annotated genes. Transcriptome and quantitative real-time PCR (qRT-PCR) analyses revealed that SMV resistance in Qihuang-1 was probably attributable to the four candidate genes (Glyma13g25920, Glyma13g25950, Glyma13g25970 and Glyma13g26000). The four candidate genes identified in this study can be used in further studies to investigate the role of resistance genes in conferring SC3 resistance in Qihuang-1.

Inheritance of Resistances to Soybean Mosaic Virus Strains SC4 and SC8 in Soybean: Inheritance of Resistances to Soybean Mosaic Virus Strains SC4 and SC8 in Soybean

选用我国黄淮和长江流域大豆产区发生频繁的SMV株系SC4和SC8,利用大豆抗病材料和感病材料配制抗感和抗抗杂交组合,研究抗病材料对SC4和SC8株系的遗传方式以及不同大豆材料对SMV抗性基因位点间的等位性关系。结果表明,接种SC4株系后,由冀LD42、徐豆1号、跃进4号、科丰1号、PI96983、晋大74、汾豆56、大白麻和齐黄22为抗源配制的9个抗感组合的F1均表现抗病,经卡方测验,F2抗感分离比例3：1,F2：3家系分离比例为1（抗）：2（分离）：1（感）,表明这些抗源均有1对基因控制对SC4株系的抗性,且抗病表现为显性;5个抗抗组合的F1均表现抗病,F2群体分离比例15（抗）：1（感）,表明大白麻与汾豆56、科丰1号和齐黄1号携带抗SC4的基因是不等位的,冀LD42与汾豆56,晋大74与中作229是不等位的。接种SC8株系后,用齐黄1号、中作229、NY58、科丰1号、PI96983、晋大74、汾豆56、大白麻和齐黄22为抗源配制的抗感组合杂交后代分离符合1对基因的分离比例且F1均表现抗病,说明这些品种对SC8株系的抗性也均由1对显性基因控制。抗抗组合晋大74×汾豆56接种SC8株系后的F2群体全部表现抗病,F2：3家系没有抗感分离,表明抗病品种晋大74与汾豆56携带的抗病基因是等位的;齐黄1号×科丰1号、大白麻×汾豆56的F2群体分离比例15（抗）：1（感）,表明抗病亲本齐黄1号与科丰1号、大白麻与汾豆56携带抗SC8的基因是不等位的,而且独立遗传。

Fine Mapping of Resistance Genes to SMV Strains SC6 and SC17 in Soybean

SMV strains SC6 and SC17 were prevalent in the North China and the Yangtze Valleys soybean production regions. Two soybean cultivars Q0926 and Zhongdou 35, which were resistant to SC6 and SC17, were respectively crossed with Nannong 1138-2 and Nannongcaidou 5, which were susceptible to SC6 and SC17, to determine inheritance of resistance to SC6 or SC17. Q0926 was also crossed with Zhongdou 35 to study allelic relationships of the resistance genes from the two soybean cultivars. On the basis of the results, the resistance genes to SC6 and SC17 were fine mapped. The results showed that the F 1 plants presented complete resistance, F2 population were segregated with a ratio of 3R:1S, F2:3 population were segregated with a ratio of 1R:2Seg:1S in resistant (R)×susceptible (S) crosses. These results indicated that the resistances of Q0926 and Zhongdou 35 to SC6 and SC17 were controlled by a single dominant gene respectively. The F 1 plants displayed complete resistance, and F 2 populations of the crosses Q0926×Zhongdou 35 were not segregated, indicating that the resistance genes to SC6 and SC17 were allelesor very closely linked. Genetic maps showed that 25 SSR markers were linked to the resistance gene to SC6 (designated R SC6 ) and the genetic distance and order of the two closest SSR markers to R SC6 were BARCSOYSSR_02_0617 (0.775 cM)-R SC6BARCSOYSSR_02_0621 (0.519 cM). The 38 SSR markers were linked to the resistance gene to SC17 (designated R SC17 ) and the genetic distance and order of the two closest SSR markers to R SC17 were BARCSOYSSR_02_0622 (0.264 cM)-R SC17BARCSOYSSR_02_0627 (0.262 cM), their corresponding physical intervals were 52 kb and 60 kb. The studies on inheritance of resistance to SMV provide a theoretical guidance to programs of resistance breeding to SMV. Fine map of resistance genes laid the foundation for molecular marker-assisted selection and map-based cloning of resistance genes.

Spatio-temporal characterisation of changes in the resistance of widely grown soybean cultivars to Soybean mosaic virus across a century of breeding in China

Abstract. Soybean mosaic virus (SMV) causes significant yield losses and seed-quality deterioration in the soybean (Glycine max (L.) Merr.) growing areas of China, and breeding disease-resistant cultivars is the most common approach for controlling the spread of the disease and the destruction of soybean crop. In this study, 97 widely grown soybean cultivars representing nine decades (1923–2006) of breeding from the four main soybean-producing subregions in China (Northern Heilongjiang (NH), Mid-Southern Heilongjiang (MSH), Jilin-Liaoning (JL) and Yellow–Huai-Hai River Valleys (YHH)) were inoculated with six prevalent SMV strains: SC3, SC7, SC8, SC11, SC15 and SC18. The average disease index (ADI) of the six SMV strains ranged from 26.95 to 48.97, and the numbers of resistant and susceptible cultivars to the six SMV strains ranged from 27 (27.8%) to 64 (66.0%) and 33 (34.0%) to 70 (72.2%), respectively. The ADIs of cultivars from NH, MSH, JL and YHH were 50.82, 47.27, 43.10 and 33.05, respectively. Soybean cultivars released in the 1940s and 1960s had the highest and lowest ADI values, 53.95 and 32.03, respectively. From NH and JL, all individual strain disease index (DI) values exhibited decreasing trend over time, but no decreasing trend in DI values was observed from MSH. From YHH, DI values for SC3 and SC18 displayed apparent increasing trend over time, and DI values for SC15 showed an obvious decreasing trend. In all, 24 soybean cultivars were identified as having broad-spectrum resistance, with ADI values ranging from 0.80 to 35.52 for the six SMV strains, and 13 soybean cultivars were identified as highly resistant to at least one SMV strain. The findings of this study will contribute to monitoring the pattern of spatio-temporal variation in SMV resistance in different soybean-producing areas of China and facilitate conventional and molecular breeding programs for SMV resistance in soybean.

Marker-assisted pyramiding of soybean resistance genes Rsc4, Rsc8, and Rsc14Q to soybean mosaic virus

Abstract Soybean mosaic virus (SMV) is one of the major viral pathogens affecting soybean crops worldwide. Three SMV resistance genes, RSC4, RSC8, and RSC14Q, have been identified and mapped on soybean chromosomes 14, 2, and 13 from Dabaima, Kefeng 1, and Qihuang 1 cultivars, respectively. Soybean cultivar Nannong 1138-2 is widely grown in the Yangtze River Valley of China. In this study, crosses were made between Qihuang 1×Kefeng 1 and Dabaima×Nannong 1138-2. Ten simple sequence repeat (SSR) markers linked to three resistance loci (RSC4, RSC8, and RSC14Q) were used to assist pyramided breeding. Pyramided families containing three resistance loci (RSC4, RSC8, and RSC14Q) were evaluated by inoculating them with 21 SMV strains from China. Results indicated that the 10 markers can be used effectively to assist the selection of resistant individuals containing RSC4, RSC8, and RSC14Q A total of 53 F6 plants were confirmed to contain three homozygous alleles conferring resistance to SMV. Five F7 homozygous pyramided families exhibited resistance to 21 strains of SMV and showed desirable agronomic traits using dual selection. The strategy of pyramiding resistance gene derived from different varieties has practical breeding value in providing broad-spectrum resistance against the existing strains of SMV in China.