Differential Detection of Alternaria alternata Haplotypes Isolated from Carya illinoinensis Using PCR-RFLP Analysis of Alt a1 Gene Region

Abstract

Alternaria black spot disease on pecan is caused by the opportunistic pathogen Alternaria alternata and poses a serious threat to the local South African and global pecan industry. Several diagnostic molecular marker applications have been established and used in the screening of various fungal diseases worldwide. The present study investigated the potential for polymorphism within samples of A. alternata isolates obtained from eight different geographical locations in South Africa. Pecan (Carya illinoinensis) leaves, shoots, and nuts-in-shuck with Alternaria black spot disease were sampled, and 222 A. alternata isolates were retrieved. For rapid screening to identify Alternaria black spot pathogens, polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis of the Alternaria major allergen (Alt a1) gene region was used, followed by the digestion of the amplicons with HaeIII and HinfI endonucleases. The assay resulted in five (HaeIII) and two (HinfI) band patterns. Unique banding patterns from the two endonucleases showed the best profile and isolates were grouped into six clusters using a UPGMA (unweighted pair group method with arithmetic averages) distance matrix (Euclidean) dendrogram method on R-Studio. The analysis confirmed that the genetic diversity of A. alternata does not depend on host tissues or the pecan cultivation region. The grouping of selected isolates was confirmed by DNA sequence analysis. The Alt a1 phylogeny corroborated no speciation within the dendrogram groups and showed 98–100% bootstrap similarity. This study reports the first documented rapid and reliable technique for routine screening identification of pathogens causing Alternaria black spot in South Africa.

In Vitro Evaluation of Azoxystrobin, Boscalid, Fentin-Hydroxide, Propiconazole, Pyraclostrobin Fungicides against Alternaria alternata Pathogen Isolated from Carya illinoinensis in South Africa

“…The production of pecans ( Carya illinoinensis ) in South Africa (SA) currently shows yield limitations mainly due to the development of diseases [ 1 , 2 ]. Alternaria black spot (ABS), caused by Alternaria alternata , is one of the more prevalent diseases in SA pecans [ 3 , 4 ]. At present, no ABS disease on pecans caused by species of Alternaria has been reported elsewhere in the world.…”

Random amplified microsatellites (RAMS) analysis ascertains genetic variation of Alternaria alternata causing black spot disease on Carya illinoinensis in South Africa

“…Restriction fragment length polymorphisms (RFLPs) outlined the distribution of Alternaria species causing early blight of potato ( Solanum tuberosum ) and tomato ( Solanum lycopersicum ) in Algeria and India ( Ayad et al, 2019 ; Kaur T. et al, 2020 ). RFLPs was also employed to screen a large collection of A. alternata isolates causing black spot of pecan ( C. illinoinensis ) in South Africa without the need for expensive sequencing ( Achilonu et al, 2023b ). However, RFLP molecular markers have limited ability to discriminate between genetically similar isolates within A. alternata populations ( Pryor and Michailides, 2002 ).…”