Rapid DNA-genotyping system targeting ten loci for resistance to blast disease in rice

Dynamics of spatial and temporal population structure of Pyricularia oryzae in Taiwan

BACKGROUND

To gain a better understanding of how Pyricularia oryzae population shifts is important for selecting suitable resistance genes for rice breeding programs. However, the relationships between P. oryzae pathogenic dynamics, geographic distribution, rice varieties, and timeline are not well studied.

RESULTS

Resistance genes Piz-5, Pi9(t), Pi12(t), Pi20(t), Pita-2, and Pi11 showed stable resistance to the Taiwan rice blast fungus over 8 years of observations. Furthermore, 1749 rice blast isolates were collected from 2014 to 2021 and categorized into five pathotype clusters based on their correlation analysis between the geographic sources and virulence of Lijiangxintuanheigu monogenic lines. A detailed map of their distributions in Taiwan is presented. Isolates collected from the western region of Taiwan had greater pathotype diversity than those from the east region. Isolates collected from the subtropical region had greater diversity than those from the tropical region. Rice cultivars carrying Pik alleles were highly susceptible to pathotype L4. Cultivars with Piz-t were highly susceptible to pathotype L5, and those with Pish were highly susceptible to pathotype L1. The geographical distribution of each pathotype was distinct, and the population size of each pathotype fluctuated significantly each year.

CONCLUSION

The regional mega cultivars significantly impact the evolution of Pyricularia oryzae in Taiwan within the span of 8 years. However, the annual fluctuation of pathotype populations likely correlate to the rising annual temperatures that selected pathotype clusters by their optimal growth temperature. The results will provide useful information for effective disease management, and enable the R-genes to prolong their function in the fields. © 2023 Society of Chemical Industry.

Rapid and easy construction of a simplified amplicon sequencing (simplified AmpSeq) library for marker-assisted selection

Marker-assisted selection (MAS) is fundamental for plant breeding programs, as it can identify desirable seedlings at a young stage and reduce the cost, time and space needed for plant maintenance, especially for perennial crops. To facilitate the process of genotyping, which is time consuming and laborious, we developed a simplified amplicon sequencing (simplified AmpSeq) library construction method for next-generation sequencing that can be applied to MAS in breeding programs. The method is based on one-step PCR with a mixture of two primer sets: the first consisting of tailed target primers, the second of primers that contain flow-cell binding sites, indexes and tail sequences complementary to those in the first set. To demonstrate the process of MAS using s implified AmpSeq, we created databases of genotypes for important traits by using cultivar collections including triploid cultivars and segregating seedlings of Japanese pear (Pyrus pyrifolia Nakai), Japanese chestnut (Castanea crenata Sieb. et Zucc.) and apple (Malus domestica Borkh.). Simplified AmpSeq has the advantages of high repeatability, ability to estimate allele number in polyploid species and semi-automatic evaluation using target allele frequencies. Because this method provides high flexibility for designing primer sets and targeting any variant, it will be useful for plant breeding programs.

Identification of Elite R-Gene Combinations against Blast Disease in Geng Rice Varieties

Rice blast, caused by the Magnaporthe oryzae fungus, is one of the most devastating rice diseases worldwide. Developing resistant varieties by pyramiding different blast resistance (R) genes is an effective approach to control the disease. However, due to complex interactions among R genes and crop genetic backgrounds, different R-gene combinations may have varying effects on resistance. Here, we report the identification of two core R-gene combinations that will benefit the improvement of Geng (Japonica) rice blast resistance. We first evaluated 68 Geng rice cultivars at seedling stage by challenging with 58 M. oryzae isolates. To evaluate panicle blast resistance, we inoculated 190 Geng rice cultivars at boosting stage with five groups of mixed conidial suspensions (MCSs), with each containing 5-6 isolates. More than 60% cultivars displayed moderate or lower levels of susceptibility to panicle blast against the five MCSs. Most cultivars contained two to six R genes detected by the functional markers corresponding to 18 known R genes. Through multinomial logistics regression analysis, we found that Pi-zt, Pita, Pi3/5/I, and Pikh loci contributed significantly to seedling blast resistance, and Pita, Pi3/5/i, Pia, and Pit contributed significantly to panicle blast resistance. For gene combinations, Pita+Pi3/5/i and Pita+Pia yielded more stable pyramiding effects on panicle blast resistance against all five MCSs and were designated as core R-gene combinations. Up to 51.6% Geng cultivars in the Jiangsu area contained Pita, but less than 30% harbored either Pia or Pi3/5/i, leading to less cultivars containing Pita+Pia (15.8%) or Pita+Pi3/5/i (5.8%). Only a few varieties simultaneously contained Pia and Pi3/5/i, implying the opportunity to use hybrid breeding procedures to efficiently generate varieties with either Pita+Pia or Pita+Pi3/5/i. This study provides valuable information for breeders to develop Geng rice cultivars with high resistance to blast, especially panicle blast.

Genetic Variation of Blast (Pyricularia oryzae Cavara) Resistance in the Longistaminata Chromosome Segment Introgression Lines (LCSILs) and Potential for Breeding Use in Kenya

In Kenya's rice-growing areas, Basmati varieties have been produced in monoculture since the late 1980s. This has resulted in the breakdown of the resistance (R) gene-mediated response of the local Basmati varieties to blast disease caused by Pyricularia oryzae. To improve blast resistance in Kenyan Basmati varieties, continuous identification of R genes and suitable breeding materials for Basmati are necessary. Longistaminata chromosome segment introgression lines (LCSILs) with the Kernel Basmati genetic background, developed using a rice line called potential low-input adaptable-1 (pLIA-1) derived from a cross between Taichung 65 (T65) (a rice variety in the Japonica Group) and O. longistaminata, are expected to contain useful blast R genes derived from O. longistaminata or T65. In this study, we investigated the genetic variation of blast R genes in LCSILs and their parents by using a new international differential system for designating blast races based on the gene-for-gene theory and molecular characterization using single nucleotide polymorphism (SNP) markers. LCSILs and their parents were classified into three groups-A, B1, and B2-based on reaction patterns to the standard differential blast isolates (SDBIs). Group A, including pLIA-1, showed the highest resistance in all groups, followed by groups B1 and B2. Kernel Basmati in group B1 was considered to possess Pik-p or Pi7(t), Pi19(t), and other unknown R genes. In addition to these R genes, LCSIL 6, 12, 27, 28, and 40, in group A, were determined to possess one of Pish, Piz-t, or both genes that confer resistance to the Kenyan blast races. These lines can be used for efficiently pyramiding blast R genes in the local Basmati varieties.