Allele Mining and Selective Patterns of Pi9 Gene in a Set of Rice Landraces from India

Abstract

Allelic variants of the broad-spectrum blast resistance gene, Pi9 (nucleotide binding site-leucine-rich repeat region) have been analyzed in Indian rice landraces. They were selected from the list of 338 rice landraces phenotyped in the rice blast nursery at central Rainfed Upland Rice Research Station, Hazaribag. Six of them were further selected on the basis of their resistance and susceptible pattern for virulence analysis and selective pattern study of Pi9 gene. The sequence analysis and phylogenetic study illustrated that such sequences are vastly homologous and clustered into two groups. All the blast resistance Pi9 alleles were grouped into one cluster, whereas Pi9 alleles of susceptible landraces formed another cluster even though these landraces have a low level of DNA polymorphisms. A total number of 136 polymorphic sites comprising of transitions, transversions, and insertion and deletions (InDels) were identified in the 2.9 kb sequence of Pi9 alleles. Lower variation in the form of mutations (77) (Transition + Transversion), and InDels (59) were observed in the Pi9 alleles isolated from rice landraces studied. The results showed that the Pi9 alleles of the selected rice landraces were less variable, suggesting that the rice landraces would have been exposed to less number of pathotypes across the country. The positive Tajima’s D (0.33580), P > 0.10 (not significant) was observed among the seven rice landraces, which suggests the balancing selection of Pi9 alleles. The value of synonymous substitution (-0.43337) was less than the non-synonymous substitution (0.78808). The greater non-synonymous substitution than the synonymous means that the coding region, mainly the leucine-rich repeat domain was under diversified selection. In this study, the Pi9 gene has been subjected to balancing selection with low nucleotide diversity which is different from the earlier reports, this may be because of the closeness of the rice landraces, cultivated in the same region, and under low pathotype pressure.

Restructuring plant types for developing tailor‐made crops

“…A smaller set of core/minicore collection accessions will be easy to phenotype and genotype (Kumar et al ., 2020; Upadhyaya et al ., 2019). Mining out novel genetic variants in the wild germplasm and landraces has been an excellent strategy for identifying development and architecture‐related allelic variants that generally get lost during domestication (Imam et al ., 2016; Mishra et al ., 2016). Precise phenotyping in control and field conditions and rapid, cost‐effective genotyping using fluorescence‐, array‐ and sequencing‐based techniques are key to delineate trait‐regulating allelic variants.…”

Understanding the Dynamics of Blast Resistance in Rice-Magnaporthe oryzae Interactions

“…To study allelic variants and flanking sequence of Pi-ta, 159 geographically diverse accessions of Oryza species (AA genome) have been used [ 288 ]. The Pi-ta and Pi9 alleles have been studied extensively in Indian landraces [ 289 , 290 ]. Five unique and novel Pi-ta variants were identified from local landraces of rice.…”

Recent Progress in Rice Broad-Spectrum Disease Resistance

“…Unlike most blast R genes, Ptr , which is required for broad-spectrum blast resistance mediated by R genes Pita and Pita2 , encodes a four Armadillo (ARM) repeat protein. Furthermore, more alleles or natural variation of broad-spectrum blast resistance R genes have been investigated, including geographically distinct and domain-specific sequence variations of Pib , novel alleles of Pik locus Pi1 , Pike, and Pikg , Pi54 alleles, novel Pi21 haplotypes, and novel alleles of Pi2/9 locus [ 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 ]. In addition, four broad-spectrum resistance R genes, Pi-hk1 , Pi57 ( t ), Pi65 ( t ), and Pi69 ( t ), were finely mapped in the past 10 years [ 23 , 24 , 25 , 26 ].…”