Genetic Studies of Pearl Millet [Pennisetum Glaucum (L.) R. Br.] For Resistance to Striga Hermonthica

Abstract

Pearl millet is a major food crop in the northern part of Nigeria. However, its production has been constrained due to several factors, among them is Striga hermonthica. To understand pearl millet farmers’ varietal preference traits, production constraints and knowledge of Striga infestation, a participatory rural appraisal was conducted across six districts in three local government areas of Jigawa State in Nigeria. Data were sourced using a semi-structured questionnaire among 143 farmers that involved focus group discussion sessions were used to verify information gathered from the questionnaires. Results showed that resistance to Striga infestation, resistance to downy mildew, tolerance to shattering, lodging tolerance and good quality local beverage were the most preferred traits by farmers. Major production constraints identified by farmers across the study areas were poor soil fertility, Striga infestation, downy mildew, and high cost of labour. Farmers were well informed about Striga as a menace and emphasized that it is likely to become worse unless controlled. A germplasm collection composed of 240 accessions of pearl millet were screened under natural Striga hermonthica infestation in the field. The results showed significant variation in the resistance of pearl millet genotypes to Striga. Fifteen genotypes identified as the most resistant were free of emerged Striga shoots, 10 genotypes supported 1-4 Striga shoots but with appreciable yield and 15 genotypes with 1-4 Striga shoots and low grain yield. Principal Component and cluster analyses grouped these genotypes into three main clusters as medium yielding tolerant to Striga, low yielding susceptible to Striga and medium to high yielding resistant to Striga. The high level of resistance observed in some breeding lines enabled the selection of suitable parents for population development. Two resistant and two susceptible to Striga genotypes selected from the field screening were used to study the gene effects controlling resistance to Striga in pearl millet. Six basic generations each were developed for the two sets of crosses and evaluated for resistance to Striga in the field. Results showed significant variation for resistance to Striga among genotypes and genotype by environments interactions. Additive and non-additive of gene actions were responsible for three indices of Striga resistance assessed; area under Striga number progress curve, Striga damage rating and the number of tillers and these varied from cross to cross and from environment to environment. In addition, a genome-wide association study (GWAS) aimed at identifying genomic loci and SNP markers associated with Striga resistance was performed using 188 pearl millet lines and 4802 SNP markers. Genotyping was achieved using the Diversity Array Technology (DArT) high-throughput genotyping-by-sequencing (GBS). Results revealed the presence of two sub-groups and a third mixed group were identified among the lines tested. Sixteen significant SNP markers associated with area under Striga number progress curve (ASNPC) were identified on five chromosomes; 2, 3, 4, 5 and 7 across all the three locations. The QTLs on chromosome 5, 2 and 3 accounted for 11 to 13% phenotypic variation. Six significant SNPs were detected for tiller number and two of these SNPs located on chromosome 1 and 5 were consistent across two locations. New SNPs were identified for Striga resistance and number of tillers (NTL). These need to be validated and fine-mapped for their use in marker-assisted selection for Striga resistance in pearl millet. The study further investigated genetic variation in production of strigolactone and tillering ability in ten pearl millet lines selected from the mapping population used for GWAS. Two major strigolactones; orobanchol and 5-deoxystrigol were identified and characterized. Five pearl millet lines; 16_R, 153_R, 96_R, 172_S and 140_S produced the highest level of orobanchol. All the test lines produced significantly lower 5-deoxystrigol than IBL (susceptible control) except 158_R. The susceptible lines 172_S and140_S induced highest Striga germination. The lines 153_R and 196_R that produced high orobanchol had the highest number of tillers. There is a positive correlation between orobanchol production and tillers production for 153_R and 96_R and a negative correlation between orobanchol and 5-deoxystrigol. A weak positive correlation was observed between Striga germination and orobanchol. These results demonstrated that genetic variability in the number of tillers is related to genetic variation in Strigolactone production and could be used as a morphological marker to select lines with low susceptibility to Striga infestation.