QTL Mapping of Charcoal Rot Resistance in PI 567562A Soybean Accession

Abstract

Charcoal rot of soybean [Glycine max (L.) Merr.], caused by the soilborne fungus Macrophomina phaseolina (Tassi) Goid., has ranked among the most important soybean diseases in the United States. Disease management is typically done in a multifaceted approach through crop rotation, tillage, irrigation, and seed treatments aimed at minimizing damage caused by the pathogen. Development of genetic resistance to charcoal rot appears to be the most efficient strategy to control the disease; however, there are no reports of genetic regions associated with resistance to the disease. The objective of this study was to identify quantitative trait loci (QTLs) governing resistance to charcoal rot in soybean using a biparental population of PI 567562A (resistant) × PI 567437 (susceptible). A total of 140 F2–derived lines were genotyped with 5403 single nucleotide polymorphism (SNP) markers covering 20 chromosomes, of which 2283 were polymorphic. Resistance to charcoal rot was evaluated in the F2:3 lines using the cut‐stem inoculation technique under greenhouse conditions. The QTL mapping analysis indicated one QTL on chromosome 15 explaining 29.4% of phenotypic variation, and two QTLs on chromosome 16 explaining 25.4 and 8.4% of phenotypic variation for resistance to M. phaseliona. To our knowledge, this is the first report of genomic regions harboring resistance to charcoal rot in soybean, and it may facilitate breeding and molecular engineering progress to combat charcoal rot disease in the future.

Breeding for disease resistance in soybean: a global perspective

“…Even though moderately resistant cultivars have been identified, the lack of identifying a complete resistance has delayed the progress to better understanding the genetics of resistance. Most of those genotypes were screened using at least one of the six screening methods for the disease assessment including: colony-forming unit index (CFUI); root stem severity (RSS); percent height of stem discoloration (PHSD); foliar symptoms (FS); cut-stem inoculation method; and seed plate assay (SPA) (Mengistu et al 2007 ; Twizeyimana et al 2012 ; da Silva et al 2019 ). Of all these methods, CFUI and RSS have been the stay methods for charcoal rot assessment currently used in the field.…”

“…Recently, QTL mapping and GWA studies were reported on multiple genomic regions harboring horizontal resistance to charcoal rot in soybean, which may be used to facilitate breeding and MAS against this pathogen (Table 14 ) (Coser et al 2017 ; da Silva et al 2019 , 2020 ; Ghorbanipour et al 2019 ). More efforts are needed to identify complete resistant sources and develop tightly linked molecular markers to facilitate breeding resistant varieties.…”

“…14) ss715618004 219,725 a2 Field test and cut-stem inoculation technique/isolate from Iowa soybean field USDA PI lines (459) – – Coser et al ( 2017 ) – 2,442,086 a2 Cut-stem inoculation technique/isolate Conway F2:3 (140) – PI 567562A da Silva et al ( 2020 ) MLG E (Chr. 15) Gm15_01842053 and Gm15_03051337 1,842,060 a2 Cut-stem inoculation technique/isolate Conway F2:3 (140) 29.4% PI 567562A da Silva et al ( 2019 ) MLG J (Chr. 16) Gm16_28961127 and Gm16_30493887 29,328,591–30,862,012 a2 Cut-stem inoculation technique/isolate Conway F2:3 (140) 25.4% PI 567562A da Silva et al ( 2019 ) Gm16_35973543 and Gm16_37078478 36,476,386–37,570,986 a2 Cut-stem inoculation technique/isolate Conway F2:3 (140) 8.84% PI 567562A da Silva et al ( 2019 ) MLG G (Chr.…”

Macrophomina phaseolina: General Characteristics of Pathogenicity and Methods of Control

“…Notably, the identification and mapping of QTLs associated with resistance to M. phaseolina, revealed candidate genes with potential for further functional genomics analysis and it may facilitate breeding and molecular engineering progress against this pathogen (Srinivasa Reddy et al, 2007;Muchero et al, 2011;Tomar et al, 2017;Mahmoud et al, 2018;da Silva et al, 2019).…”

Molecular Breeding to Overcome Biotic Stresses in Soybean: Update

“…In a recent study conducted by da Silva et al [ 88 ], a total of 140 F 2 -derived lines from a population were developed by crossing PI 567562A (resistant) and PI 567,437 (susceptible) genotypes for identification of QTL/s linked with charcoal rot resistance in soybean. The plant population was genotyped with 5403 SNP markers covering 20 chromosomes.…”