Meta-QTL analysis and identification of candidate genes governing popping quality attributes in maize

Popcorn is a specialty maize famously savoured worldwide as snack, and genetic improvement of popping quality traits is important to meet the growing market demand. Though quantitative trait loci (QTLs) for pop-ping quality traits were reported, low resolution and inconsistent effects limits their direct deployment in targeted trait improvement. Considering the importance of popping quality, consensus and stable meta-QTL regions can be entailed in designing new cultivars with enhanced popping quality traits through genomics-assisted approaches. In the present investigation, 120 popping quality determining QTLs from 10 different reports were assembled for meta-analysis to obtain precise and consistent QTL(s) followed by identification of underlying candidate genes for popping quality. The study identified eight meta-QTLs on chromosome 1, two on chromosome 6 and one on chromosome 7 with significantly reduced confidence interval and high weightage (0.03-0.64). Of these, MpQTL-1.1, MpQTL-1.3, MpQTL-1.5, MpQTL-1.8 and MpQTL-6.2 each pos-sessed more than 4 QTLs from independent studies. Additionally, MpQTLs overlapped the chromosomal regions associated with agronomic and kernel composition traits. Functional ontology analysis of MpQTL-1.1 identified simple sequence repeat (SSR) marker umc2012 associated with transcription factor'NACTF53' that contained a cis-acting CBF-domain. The marker also significantly differentiated normal maize and popcorn inbreds for popping quality traits. In addition, gene models Zm00001eb002590, Zm00001eb002620 and Zm00001eb002650 lying within 0.14 Mb from umc2012 were involved in starch and other carbohydrate metabolism. The validated marker umc2012 within MpQTL-1.1 can be used for marker-assisted introgression of popping quality traits. This is the first comprehensive report on meta-analysis and validation of markers for popping quality traits in maize. & COPY; 2023 SAAB. Published by Elsevier B.V. All rights reserved.