Characterization of Sugarcane Mosaic Virus Scmv1 and Scmv2 Resistance Regions by Regional Association Analysis in Maize

SCMV was first reported in China in 1968 and is responsible for a yield reduction of approximately 2500 kg per hectare in Henan province. The virus is transmitted by aphids and cannot be controlled by chemicals, making cultivation of resistant varieties the most effective way to control SCMV infection. SCMV resistant lines have been identified, indicating that genetic resistance is an economic way to control SCMV. Three lines, D21, D32, and FAP1360A, displayed complete resistance to SCMV among 122 early maturing European maize inbred lines. In the U.S., Pa405, B68, Oh7B, Mp339, GA209, and A239 were shown to be resistant to SCMV, while Huangzaosi, Siyi, X178, and Hai9-21 displayed complete resistance to SCMV in China. These lines were widely used for genetic analyses worldwide. The SCMV resistance genes were first located in inbred line GA209 on both arms of chromosome 6 by use of translocation lines. Research of maize resistance to SCMV was facilitated with the development of molecular markers, such as Restriction Fragment Length Polymorphism (RFLP), Amplified Fragment Length Polymorphism (AFLP), and Single Sequence Repeat (SSR) markers. The estimated number of SCMV resistance genes differs across populations, ranging from one to five. High-resolution mapping using progeny from the cross between FAP1360A (resistant) and F7 (susceptible) confirmed that Scmv1 and Scmv2 are two major SCMV resistance loci. Scmv1 is located on the short arm of chromosome 6, and Scmv2 near the centromere of chromosome 3. Scmv1 suppresses symptoms at all developmental stages, while Scmv2 functions at later stages of infection. Presence of resistance alleles at both loci, Scmv1 and Scmv2, is crucial for complete SCMV resistance. Two association panels consisting of 94 inbred lines each, from China and the U.S., were characterized for resistance to two isolates: SCMV-Seehausen and SCMV-BJ. The population structure of both association panels was analyzed using 3072 single nucleotide polymorphism (SNP) markers. The Chinese and the U.S. panel were both subdivided into two sub-populations, the latter comprised of Stiff Stalk Synthetic (SS) lines and Non Stiff Stalk Synthetic (NSS). The relative kinships were calculated using informative 2947 SNPs with minor allele frequency < 5% and missing data < 20% for the Chinese panel and 2841 SNPs with the same characteristics were used for the U.S. panel. For all traits, a Mixed Linear Model (MLM) controlling both population structure and relative kinship (Q + K) was used for association analysis. Three markers, Trx-1, STS-11, and STS-12, located in the Scmv1 region were strongly associated (P = 0.001) with SCMV resistance, and explained more than 16.0%, 10.6%, and 19.7% of phenotypic variation, respectively. 207FG003 located in the Scmv2 region was significantly associated (P = 0.001) with SCMV resistance, and explained around 18.5% of phenotypic variation.