Characterization of Diaporthe/Phomopsis species from soybean in Korea and QTL identification for host

Abstract

Phomopsis seed decay (PSD) is primarily caused by Phomopsis longicolla, along with other species in Diaporthe/Phomopsis complex in soybean. PSD has become a serious disease in soybean production with wet and warm weather worldwide. Collected soybean stems with appeared Diaporthe/Phomopsis symptoms were used to isolate pathogens of Diaporthe/Phomopsis species on soybean. Based on mycological characteristics and molecular analysis of sequences, five isolates recovered, SSLP-1 - SSLP-5, were identified into P. longicolla, the principal cause of PSD, Diaporthe phaseolorum var. caulivora (Dpc), the causal agent of soybean northern stem canker, and one uncertain species in anamorph genus Phomopsis, Phomopsis sp., respectively. The isolates of Dpc, SSLP-4, represented newly recorded pathogen on soybean in South Korea. Moreover, morphological and molecular analyses revealed that the isolate SSLP-4 was nearly identical to Dpc strains from the United States. The isolate of Phomopsis sp., SSLP-2, was referred as a new pathogen of soybean and was observed with high homologous sequence with the strains isolated from fruit trees and vegetable in different geographic areas. Pathogenicity tests on hypocotyls of soybean seedlings showed different pathogenetic levels and production ability of stromata on plants among isolates. The isolate of P. longicolla, SSLP-3, was produced a mass of pycnidia in inoculated hypocotyls, which was the most aggressive, and expected to be used as a valuable inoculum. Some resistance sources exhibited different levels of resistance to PSD only focused on PI accession genotypes. In South Korea, incidence of PSD caused by P. longicola is increasing alarmingly because of favorable environmental conditions during recent years. Based on the results of screening resistance source to PSD from elite Korean major soybean varieties and comparing with previous reported resistant genotypes PI 80837, PI 360841 and PI 562694, Taekwangkong exhibited stronger resistance to P. longicolla, however, the other Korean cultivars exhibited high level susceptible to P. longicolla with incidence of more than 70% on seeds. In addition, higher vigor in seed of Taekwangkong was further verified by testing germination rate of healthy seeds on cultures of P. longicolla. Moreover, Taekwangkong is stronger in resistance to P. longicolla than previous reported resistant genotypes, which implies Taekwangkong may have different resistance gene(s) not present in the PI resistance genotypes. The following study was conducted to identify quantitative trait loci (QTLs) for resistance to P. longicolla in Taekwangkong using SSR markers. A F8 recombinant inbred lines (RILs) population consisted of 124 lines derived from two elite Korean soybean varieties, Taekwangkong (resistant) × SS2-2 (susceptible), was used to evaluate phenotypic and genotypic data. The genetic association of single marker analysis and epistatic interactions between markers were analyzed. And analysis of QTLs was performed in the genetic map constructed with 117 SSR markers. Two new QTLs were detected at marker Satt100-Satt460 (PSD-6-1) interval on Chromosome (Chr) 6 and at marker Sat_038-Satt243 (PSD-10-2) interval on Chr 10, accounting for 46.30% and 14.06% of the phenotypic variance, respectively. QTLs associated with resistance to soybean fungal disease, SDS, soybean Sclerotinia stem rot, and Phytophthora root rot, were reported in the near regions of the new QTLs on Chrs 6 and 10, respectively. And QTLs associated with resistance to soybean insects including soybean cyst nematode (SCN), corn earworm (CEW) and bean bug are also positioned in the similar genomic regions. Moreover, SSR markers Satt100 and Sat_038 associated with PSD-6-1 and PSD-10-2 on Chrs 6 and 10 have been reported to be closely linked to the QTL or genes for flowering time and maturity, E1 and E2, respectively. In addition, both regions were also considered important for other agronomic traits in soybean. Therefore, it is possible that these regions contain different resistance genes in a cluster or the genes displaying pleiotropy. In addition, three pairs of loci with significant epistatic effect were detected and partially explained phenotypic variation, of which, marker Sat_317 was corresponding with the previous study in resistance soybean genotype MO/PSD-0259. These newly identified QTLs and closely linked markers will be helpful for exploiting resistance genes for P. longicolla in further soybean breeding studies.