Mapping QTLs for Pyricularia leaf spot, nematode resistance, and yield related traits in pearl millet [Cenchrus americanus (L.) Morrone]

Authors: VUTLA, SAIRAM - Fort Valley State University; Knoll, Joseph; SANKURATRI, ANVESH - Fort Valley State University; NAYAK, RISHA - Fort Valley State University; LIU, LEMEI - Virginia Tech; CHEE, PENG - University Of Georgia; KARTHIKEYAN, RAGHUPATHY - Clemson University; FAKRUDIN, BASHASAB - University Of Horticultural Sciences; THUDI, MAHENDAR - Fort Valley State University; TIMPER, PATRICIA - Retired ARS Employee; Harris-Shultz, Karen; WALLACE, JASON - University Of Georgia; SINGH, HARI - Fort Valley State University; SINGH, BHARAT - Fort Valley State University; PUNNURI, SOMASHEKHAR - Fort Valley State University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/9/2025
Publication Date: 6/30/2025
Citation: Vutla, S., Knoll, J.E., Sankuratri, A., Nayak, R.G., Liu, L., Chee, P.W., Karthikeyan, R., Fakrudin, B., Thudi, M., Timper, P., Harris-Shultz, K.R., Wallace, J.G., Singh, H., Singh, B., Punnuri, S.M. 2025. Mapping QTLs for Pyricularia leaf spot, nematode resistance, and yield related traits in pearl millet [Cenchrus americanus (L.) Morrone]. Frontiers in Plant Science. 16:1588485. https://doi.org/10.3389/fpls.2025.1588485.
DOI: https://doi.org/10.3389/fpls.2025.1588485

Interpretive Summary: Pearl millet is the sixth most important cereal globally, and is used for forage and feed purposes in the US. With an objective to identify the genomic regions governing important physiological, agronomic and yield related traits, a mapping population derived from the cross between Tift 99D2B1 × Tift 454 was assessed for various traits in the field during 2006, 2007, and 2013. In addition, the population was assessed for root-knot nematode resistance in the greenhouse during 2008. Using high-density next-generation sequencing technology, a genetic map was developed with 505 DNA marker loci. We then used a statistical technique known as composite interval mapping (CIM) to associate physical traits with specific regions of the pearl millet genome. Forty five quantitative trait loci (QTLs) for eight traits (plant height, stem diameter, days to heading, panicle diameter, panicle length, 1000 seed weight, Pyricularia leaf spot disease, and root-knot nematode egg mass) were identified. The QTLs explained 6.31 to 32.51% of the variation observed in the traits studied and showed consistent effects over different environments. Plant height and days to heading QTLs were colocalized on two linkage groups (LGs), showing maturity and plant height are linked and influence each other like other cereal crops. Interestingly, a group of QTLs linked to plant height, stem diameter, panicle diameter and panicle length were colocalized to the same location on LG3 indicating breeding for one trait simultaneously improves the other trait. The markers and genes identified in the present study can be used in developing high yielding pearl millet varieties using genomics-assisted breeding.

Technical Abstract: Pearl millet [Cenchrus americanus (L.) Morrone, formerly Pennisetum glaucum (L.) R. Br.] is the sixth most important cereal, known for forage and feed purpose in the US. With an objective to identify the genomic regions governing important physiological, agronomic and yield related traits, the recombinant inbred line (RIL) population derived from the cross between Tift 99D2B1 × Tift 454 was phenotyped in field during 2006, 2007 and 2013. In addition, the population was also phenotyped for root-knot nematode resistance in the greenhouse during 2008. Using genotyping-by-sequencing (GBS) based single nucleotide polymorphism (SNP) markers, a genetic map developed with 505 loci was used in Quantitative Trait Loci (QTL) mapping for key agronomic traits and nematode resistance. Using composite interval mapping (CIM) in QTL Cartographer, we identified 45 QTLs for eight traits (plant height, stem diameter, days to heading, panicle diameter, panicle length, 1000 seed weight, pyricularia leaf spot disease and, root-knot nematode egg mass) on LG1, LG2, LG3, LG5, LG6 and LG7 of pearl millet. The QTLs explained 6.31 to 32.51% of phenotypic variations for the traits studied and showed consistent QTLs over different years and locations. Plant height and days to heading were colocalized on LG2 and LG5 showing maturity and plant height are linked and influence each other like other cereal crops. Interestingly, the maximum number of QTLs, 5 of 19 QTLs linked to plant height, stem diameter, panicle diameter and panicle length were colocalized to same locations on LG3 indicating breeding for one trait simultaneously improves the other trait. Breeding for co-localized QTLs for traits like plant height, stem diameter linked to panicle morphology traits that are correlated with yield, can be improved through genomics-assisted breeding. The markers and genes identified in the present study can be used in developing high yielding pearl millet varieties using genomics-assisted breeding.