RESUMEN
BACKGROUND: Powdery mildew (PM) is one of the important soybean diseases, and host resistance could practically contribute to soybean PM management. To date, only the Rmd locus on chromosome (Chr) 16 was identified through traditional QTL mapping and GWAS, and it remains unclear if the bulk segregant RNA-Seq (BSR-Seq) methodology is feasible to explore additional PM resistance that might exist in other varieties. RESULTS: BSR-Seq was applied to contrast genotypes and gene expressions between the resistant bulk (R bulk) and the susceptible bulk (S bulk), as well as the parents. The ∆(SNP-index) and G' value identified several QTL and significant SNPs/Indels on Chr06, Chr15, and Chr16. Differentially expressed genes (DEGs) located within these QTL were identified using HISAT2 and Kallisto, and allele-specific primers (AS-primers) were designed to validate the accuracy of phenotypic prediction. While the AS-primers on Chr06 or Chr15 cannot distinguish the resistant and susceptible phenotypes, AS-primers on Chr16 exhibited 82% accuracy prediction with an additive effect, similar to the SSR marker Satt431. CONCLUSIONS: Evaluation of additional AS-primers in the linkage disequilibrium (LD) block on Chr16 further confirmed the resistant locus, derived from the resistant parental variety 'Kaohsiung 11' ('KS11'), not only overlaps with the Rmd locus with unique up-regulated LRR genes (Glyma.16G213700 and Glyma.16G215100), but also harbors a down-regulated MLO gene (Glyma.16G145600). Accordingly, this study exemplified the feasibility of BSR-Seq in studying biotrophic disease resistance in soybean, and showed the genetic makeup of soybean variety 'KS11' comprising the Rmd locus and one MLO gene.
Asunto(s)
Resistencia a la Enfermedad , Glycine max , Glycine max/genética , RNA-Seq , Alelos , Mapeo Cromosómico/métodos , Fenotipo , Resistencia a la Enfermedad/genética , Erysiphe , Enfermedades de las Plantas/genéticaRESUMEN
Aphanomyces root rot, caused by Aphanomyces euteiches, causes severe yield loss in field pea (Pisum sativum). The identification of a pea germplasm resistant to this disease is an important breeding objective. Polygenetic resistance has been reported in the field pea cultivar '00-2067'. To facilitate marker-assisted selection (MAS), bulked segregant RNA-seq (BSR-seq) analysis was conducted using an F8 RIL population derived from the cross of 'Carman' × '00-2067'. Root rot development was assessed under controlled conditions in replicated experiments. Resistant (R) and susceptible (S) bulks were constructed based on the root rot severity in a greenhouse study. The BSR-seq analysis of the R bulks generated 44,595,510~51,658,688 reads, of which the aligned sequences were linked to 44,757 genes in a reference genome. In total, 2356 differentially expressed genes were identified, of which 44 were used for gene annotation, including defense-related pathways (jasmonate, ethylene and salicylate) and the GO biological process. A total of 344.1 K SNPs were identified between the R and S bulks, of which 395 variants were located in 31 candidate genes. The identification of novel genes associated with partial resistance to Aphanomyces root rot in field pea by BSR-seq may facilitate efforts to improve management of this important disease.
Asunto(s)
Aphanomyces , Aphanomyces/genética , Pisum sativum/genética , Pisum sativum/metabolismo , Fitomejoramiento , Enfermedades de las Plantas/genética , Sitios de Carácter CuantitativoRESUMEN
Although the genetics and preliminary mapping of the cabbage yellow-green-leaf mutant YL-1 has been extensively studied, transcriptome profiling associated with the yellow-green-leaf mutant of YL-1 has not been discovered. Positional mapping with two populations showed that the yellow-green-leaf gene ygl-1 is located in a recombination-suppressed genomic region. Then, a bulk segregant RNA-seq (BSR) was applied to identify differentially expressed genes (DEGs) using an F3 population (YL-1 × 11-192) and a BC2 population (YL-1 × 01-20). Among the 37,286 unique genes, 5730 and 4118 DEGs were detected between the yellow-leaf and normal-leaf pools from the F3 and BC2 populations. BSR analysis with four pools greatly reduced the number of common DEGs from 4924 to 1112. In the ygl-1 gene mapping region with suppressed recombination, 43 common DEGs were identified. Five of the DEGs were related to chloroplasts, including the down-regulated Bo1g087310, Bo1g094360, and Bo1g098630 and the up-regulated Bo1g059170 and Bo1g098440. The Bo1g098440 and Bo1g098630 genes were excluded by qRT-PCR. Hence, we inferred that these three DEGs (Bo1g094360, Bo1g087310, and Bo1g059170) in the mapping interval may be tightly associated with the development of the yellow-green-leaf mutant phenotype.