The pathogens evolve virulence activities to infect and multiply in host, whereas in response to this the plant evolve new way (or in bred) to detect and combat pathogen attack (Sacristan et al., 2021). Therefore, the germplasm maintained are valuable. The germplasm collection act as a repertoire for range of genetic and phenotypic diversity of crop species, that may contribute to disease resistance gene (Bulli et al., 2016). The quantitative and qualitative resistance refers to the mode of inheritance. The qualitative inheritance is based on one or two major genes that segregate according to discrete phenotype (Niks et al., 2015). Quantitative disease resistance refers to an incomplete or reduced level of resistance, which is controlled by multiple quantitative trait locus (QTL) of minor to moderate effects (Gou et al., 2022). Identifying genes and genetic markers associated with resistance is crucial for developing disease resistant varieties. Breeding strategies for bacterial leaf blight resistance in rice involves use of resistance (R) genes and QTLs. Molecular markers linked to these R genes and QTLs are available, enabling marker-assisted selection (MAS) to develop resistant wheat varieties (Fatemifard et al., 2024). Linkage and QTL maps are tools for study of the genetic basis of complex traits (Ouellette et al., 2017).
QTL for disease resistance can be used to develop new varieties that are more resistant to specific pathogen causing disease. QTL sequencing may determine the genetic region associated with the trait by pooling deoxyribonucleic acid (DNA) from plant with contrasting phenotype and comparing the genotypes to identify quantitative trait loci (Takagi et al., 2013; Kim et al., 2023). The goal of QTL is to explain whether the phenotypic differences are primarily due to a few loci with large effect or due to many loci with minute effect (Miles and Wayne 2008). QTL are mapped by using genetic markers linked to QTL to infer the differences between alleles at QTL (Knapp 1994). Two QTL affect different stages of pathogenesis (infection and colonization) of Setosphaeria turcica and one of which effects the accumulation of callose and phenolic compound near the infection site (Chung et al., 2010).
A DNA marker has been used for construction of a linkage map for a range of plant species. Genetic map (also known as linkage map) indicate the position and relative genetic distance between markers along chromosomes, which are analogous to sign or landmark along a highway (Collard et al., 2005). The use of linkage map is to identify chromosomal location containing genes and QTL associated with the trait of interest; such map may then be known as QTL (or genetic) maps (Collard et al., 2005). Genetic marker is a gene or DNA sequence with a known chromosome location controlling a particular gene or trait. These markers are closely related with target gene and act as sign or flag (Collard et al., 2005; Nadeem et al., 2018). The different types of DNA markers used are single nucleotide polymorphisms (SNPs), simple sequence repeats (SSR or microsatellites), amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphisms (RFLPs) (Young 1994; Nadeem et al., 2018). Two types of DNA markers RFLP and RAPDs are widely used (Young 1994). All types of markers detect polymorphism and monitor the segregation of DNA sequence among progeny of genetic cross to construct a linkage map (Young 1994). QTL mapping provides framework for MAS of complex plant disease resistance forms and the positional cloning of partial resistance genes (Young 1996).
QTL mapping has been used for identifying the genomic region/genes associated to disease resistance traits (Gangurde et al., 2022). The principle of QTL mapping is that genes and markers segregate via chromosome recombination (crossing-over) during meiosis (sexual reproduction) thus allowing their analysis in progeny (Collard et al., 2005). Gene and markers that are close together or tightly linked will be transmitted together from parent to progeny (Collard et al., 2005). Since plant species have multiple chromosomes, independent assortment is true for majority of genes (Lubberstedt et al., 2023). During meiosis, chromosomes assort randomly into gametes, so that the segregation of alleles of one gene is independent of alleles of another gene. Genes located on different chromosomes follow independent assortment but does not hold true for the genes on the same chromosome (Semagn et al., 2006). When two genes are close together on same chromosome they do not assort independently and are said to be linked (Semagn et al., 2006). Linked genes located on the same chromosome are more likely to cosegregate i.e. being jointly transmitted to progeny more often than expected by independent assortment (Lubberstedt et al., 2023). Identification of resistance QTLs and genes on chromosomes are important for developing disease resistant plant.
References:
Bulli, P., Zhang, J., Chao, S., Chen, X. and Pumphrey, M. 2016 Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection. G3 Genes Genomes Genetics 6(8): 2237 – 2253
doi.org/10.1534/g3.116.028407
Chung, C-L., Longfellow, J. M., Walsh, E. K., Kerdieh, Z., Van Esbroeck, G., Balint-Kurti, P. and nelson, R. J. 2010 Resistance Loci Affecting Distinct Stages of Fungal Pathogenesis: Use of Introgression Lines for QTL Mapping and Characterization in the Maize- Setosphaeria turcica Pathosystem. BMC Plant Biol. 10: 103
doi: 10.1186/1471-2229-10-103
Collard, B. C. Y., Jahufer, M. Z. Z., Brouwer, J. B. and Pang, E. C. K. 2005 An Introduction to Markers, Quantitative Trait Loci (QTL) Mapping and Marker-Assisted Selection for Crop Improvement: The Basic Concepts. Euphytica 142: 169 – 196
doi: 10.1007/s10681-005-1681-5
Fatemifard, S. Z., Masoumiasl, A., Rezaei, R., Fazeli-Nasab, B., Salehi-Sardoei, A. and Ghorbanpour, M. 2024 Association between Molecular Markers and Resistance to Bacterial Blight Using Binary Logistic Analysis. BMC Plant Biol. 24(1): 670
doi: 10.1186/s12870-024-05381-1
Gangurde, S. S., Xavier, A., Naik, Y. D., Jha, U. C., Rangari, S. K., Kumar, R., Reddy, M. S. S., Channale, S., Elango, D., Mir, R. R., Zwart, R., Laxuman, C., Sudini, H. K., Pandey, M. K., Punnuri, S., Mendu, V., Reddy, U. K., Guo, B., Gangarao, N. V. P. R., Sharma, V. K., Wang, X., Zhao, C. and Thudi, M. 2022 Two Decades of Association Mapping: Insights on Disease Resistance in Major Crops. Front. Plant Sci. 13: 1064059
doi: 10.3389/fpls.2022.1064059
Gou, M., Balint-Kurti, P., Xu, M. and Yang, Q. 2022 Quantitative Disease Resistance: Multifaceted Players in Plant Defense. J. Integr. Plant Biol. 65(2): 594 – 610
doi.org/10.1111/jipb.13419
Kim, S., Lee, E., Lee, J., An, Y. J., Oh, E., Kim, J. I., Kim, S. W., Kim, M. Y., Lee, M. H. and Cho, K-S. 2023 Identification of QTLs and Allelic Effect Controlling Lignan Content in Sesame (Sesamum indicum L.) Using QTL-Seq Approach. Front. Genet. 14: 1289793
doi: 10.3389/fgene.2023.1289793
Knapp, S. J. 1994 Mapping Quantitative Trait Loci. In: “DNA Based Markers in Plants”. Phillips, R. L. and Vasil, I. K. (eds.). Springer-Science+Business Media, B. V. Chapter 4: Pages 58 – 96. Part of a Book Series: Advances in Cellular and Molecular Biology in Plants Vol. 1
Lubberstedt, T., Campbell, A., Muenchrath, D., Merrick, L. and Fei, S-Z. 2023 Linkage. In: “Crop Genetics”. Suza, W. P. and Lamkey, K. R. (eds.). Iowa State University Digital Press. Chapter 5
Miles, C. M. and Wayne, M. 2008 Quantitative Trait Locus (QTL) Analysis. Nature Education 1(1): 208
Nadeem, M. A., Nawaz, M. A., Shahid, M. Q., Dogan, Y., Comertpay, G., Yildiz, M., Hatipoglu, R., Ahmad, F., Alsaleh, A., Labhane, N, Ozkan, H., Chung, G. and Baloch, F. S. 2018 DNA Molecular Markers in Plant Breeding Current Status and Recent Advancements in Genomic Selection and Genome Editing. Biotechnol. Biotechnol. Equip. 32(2): 261 – 285
doi.org/10.1080/13102818.2017.1400401
Niks, R. E., Qi, X. and Marcel, T. C. 2015 Quantitative Resistance to Biotrophic Filamentous Plant Pathogens: Concepts, Misconceptions and Mechanisms. Annu. Rev. Phytopathol. 53: 445 – 470
doi: 10.1146/annurev-phyto-080614-115928
Ouellette, L. A., Reid, R. W., Blanchard, S. G. and Brouwer, C. R. 2017 Linkage Map View- Rendering High Resolution Linkage and QTL Maps. Bioinformatics 34(2): 306 – 307
doi: 10.1093/bioinformatics/btx576
Sacristan, S., Goss, E. M. and Eves-van der Akker, S. 2021 How Do Pathogens Evolve Novel Virulence Activities. MPMI 34(6): 576 – 586
doi.org/10.1094/MPMI-09-20-0258-IA
Semagn, K., Bjornstad, A. and Ndjiondjop, M. N. 2006 Principles, Requirements and Prospects of Genetic Mapping in Plants. African J. Biotechnol. 5(25): 2569 – 2587
Takagi, H., Yoshida, K., Kosugi, S., Natsume, S., Mitsuoka, C., Uemura, A., Utsushi, H., Tamiru, M., Takuno, S., Innan, H., Cano, L. M., Kamoun, S. and Terauchi, R. 2013 QTL-Seq: Rapid Mapping of Quantitative Trait Loci in Rice by Whole Genome Resequencing of DNA from Two Bulked Populations. The Plant Journal 74(1): 174 – 183
doi.org/10.1111/tpj.12105
Young, N. D. 1994 Constructing a Plant Genetic Linkage Map with DNA Markers. In: “DNA Based Markers in Plants”. Phillips, R. L. and Vasil, I. K. (eds.). Springer-Science+Business Media, B. V. Chapter 3: Page 39 – 57. Part of a Book Series: Advances in Cellular and Molecular Biology in Plants Vol. 1
Young, N. D. 1996 QTL Mapping and Quantitative Disease Resistance in Plants. Annu. Rev. Phytopathol. 34: 479 – 501
doi: 10.1146/annurev.phyto.34.1.479
BIOLOGICAL PROCESSES- A NATURE'S GIFT 