Major QTLs for resistance to early and late leaf spot diseases are identified on chromosomes 3 and 5 in peanut (Arachis hypogaea)

Abstract

Early and late leaf spots are the major foliar diseases of peanut responsible for severely decreased yield in the absence of intensive fungicide spray programs. Pyramiding host resistance to leaf spots in elite cultivars is a sustainable solution to mitigate the diseases. In order to determine the genetic control of leaf spot disease resistance in peanut, a recombinant inbred line population (Florida-07 x GP-NC WS16) segregating for resistance to both diseases was used to construct a SNP-based linkage map consisting of 855 loci. QTL mapping revealed three resistance QTLs for late leaf spot qLLSA05 (phenotypic variation explained, PVE=7-10%), qLLSB03 (PVE=5-7%), and qLLSB05 (PVE=15-41%) that were consistently expressed over multi-year analysis. Two QTL, qLLSA05 and qLLSB05, confirmed our previously published QTL-seq results. For early leaf spot, three resistance QTLs were identified in multiple years, two on chromosome A03 (PVE=8-12%) and one on chromosome B03 (PVE=13-20%), with the locus qELSA03_1.1 coinciding with the previously published genomic region for LLS resistance in GPBD4. Comparative analysis of the genomic regions spanning the QTLs suggests that resistance to early and late leaf spots are largely genetically independent. In addition, QTL analysis on yield showed that the presence of resistance allele in qLLSB03 and qLLSB05 loci might result in protection from yield loss caused by LLS disease damage. Finally, post hoc analysis of the RIL subpopulation that was not utilized in the QTL mapping revealed that the flanking markers for these QTLs can successfully select for resistant and susceptible lines, confirming the effectiveness of pyramiding these resistance loci to improve host-plant resistance in peanut breeding programs using marker-assisted selection.

Association of differentially expressed R-gene candidates with leaf spot resistance in peanut (Arachis hypogaea L.)

“…ELS and LLS are major diseases of peanuts and the range of severity is strongly influenced by G x E associated with many QTLs [21][22][23]. Only a few peanut genotypes have been identified as medium tolerant to leaf spot diseases and specific crosses were generated to develop more tolerant lines [8]. Marker types, such as simple sequence repeats (SSRs) and Insertions/Deletions (Indels), were applied to select leaf spot resistant lines [24,25], but validation has been difficult due to variations in leaf spot disease phenotyping (strong environmental effect, different levels of pathogen pressure, state of plant health).…”

“…Identification of major genes for disease resistance has been very elusive based on strong environmental and genetic interactions and the involvement of multiple QTLs [7][8][9]. The nature of plant and fungal interactions makes visual selections highly variable based on years and locations.…”

“…Han et al [7] identified QTLs for ELS and LLS using single nucleotide polymorphism (SNP)-based linkage map, with analysis of interval sequences indicated a major QTL for LLS resistance. Chu et al [8] identified 3 resistance QTLs on chromosome 3 and 1 on chromosome 5 evaluating recombinant inbred lines (RILs) from a population (Florida-07 × GP-NC WS16) segregating for resistance. Zhang et al [9] identified 2 QTLs on chromosome B09 that were significantly associated with ELS and LLS resistance evaluating the US mini-core peanut collection.…”

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

“…In this study, seven and four STAs identified in NAM‐T and NAM‐F, respectively, co‐located in QTL regions of PW and SW in both seasons on chromosomes A05. Chu et al () identified a QTL on B05 overlaps for pod yield and LLS resistance. Interestingly, in this study we also reported QTLs for both PW and SW in both NAM populations on B05.…”

“…The primary objective of this developed genetic resource was to share these populations with the peanut research community and to undertake high‐resolution phenotyping of these populations (Chu et al , ; Holbrook et al , ). The parents represent a wide range of agronomic, morphological and disease resistance traits, and some biparental populations have been studied for resistance to early and late leaf spot diseases (Chu et al , ; Clevenger et al , ). These two NAM populations thus could combine the strengths of both linkage and association mapping since the NAM populations have higher power QTL detection as compared with biparental mapping populations (Guo et al , ; Wang et al , ; Yu et al , ).…”