| Literature DB >> 31598076 |
Cong Nguyen Phi1, Daisuke Fujita1, Yoshiyuki Yamagata1, Atsushi Yoshimura1, Hideshi Yasui1.
Abstract
The green rice leafhopper (GRH), Nephotettix cincticeps Uhler, is a major insect pest of cultivated rice, Oryza sativa L., throughout the temperate regions of East Asia. GRH resistance had been reported in the wild species Oryza nivara but genetic basis of GRH resistance in wild rice accession has not been clarified. Here, we found a major QTL, qGRH4.2, on chromosome 4 conferred GRH resistance with 14.1 of the logarithm of odds (LOD) score explaining 67.6% of phenotypic variance in the BC1F1 population derived from a cross between the susceptible japonica cultivar 'Taichung 65' (T65) and O. nivara accession IRGC105715. qGRH4.2 has been identified as GRH6 between the markers RM5414 and C60248 in a BC3F2 population derived from two BC3F1 plants resistant to GRH. In a high-resolution mapping, the GRH6 region was delimited between the markers G6-c60k and 7L16f, and corresponded to an 31.2-kbp region of the 'Nipponbare' genome. Understanding the genetic basis of GRH resistance will facilitate the use of GRH resistance genes in marker-assisted breeding in rice.Entities:
Keywords: antibiosis test; green rice leafhopper; high-resolution mapping; rice; wild relative
Year: 2019 PMID: 31598076 PMCID: PMC6776147 DOI: 10.1270/jsbbs.19029
Source DB: PubMed Journal: Breed Sci ISSN: 1344-7610 Impact factor: 2.086
Fig. 1Breeding scheme of a population used for high-resolution mapping of GRH6. Graphical genotype of a resistant BC3F1 plant deduced from genotyping of BC3F2 plants.
Simple sequence repeat markers used for high-resolution mapping of GRH6
| Marker | Forward primer sequence (5′→3′) | Reverse primer sequence (5′→3′) | Size (bp) | Physical location (bp) |
|---|---|---|---|---|
| RM5414 | ACCATGGTTCAAGAGTGAAA | ACAGCTCAACCTGTTGAGTG | 116 | 2034580–2034695 |
| G6-5 | TCGCACGACTCTAACCATACTG | GTCATGCAACAATGGAGACG | 250 | 4191855–4192104 |
| G6-30 | GTGGGTGCTGTTAGCTCAAGT | CTGAATCCAGCTGCTCTCACT | 116 | 4301909–4302024 |
| RM8213 | AGCCCAGTGATACAAAGATG | GCGAGGAGATACCAAGAAAG | 211 | 4446034–4446244 |
| G6-c60k | AGATGGTGTGGCCTTGAGTC | CTTCAGCGTCAAGGACAGGT | 893 | 4460301–4461193 |
| sts4 | TTGGGAGATGGGAGGAGGA | CTCACCCATCTCTTCCCAT | 124 | 4463002–4463125 |
| sts2 | TGACGTGTGACGTGCACTGTAG | GGCGGCTGTATGTACTGAACTT | 213 | 4480552–4480764 |
| sts1 | TTGATGCTGCATCGTGGTGATG | GCAAATGCAGCCATCTAAGC | 154 | 4484875–4485028 |
| G6-c70k | GCAAATGCAGCCATCTAAGC | CCTCGCCACTCGATGTACTA | 922 | 4484875–4485796 |
| 7L16f | AAATGGCTAATGCGGTTCTG | GTTGCAAATGCACGACACAT | 457 | 4491085–4491541 |
| G6-9 | GCCGTGGAGAAGAAGCTGTA | CCTAGACCTCATCCCCTTCC | 140 | 4674853–4674992 |
| G6-16 | GCGGTGAGATAGATGGATGG | CCTCGTAAACCCTGTCCTTCA | 224 | 5677175–5677398 |
| C60248 | AACAAGATGTCCAGTAACCC | GAGATTTGGAGAGGCTTTAG | 208 | 6638534–6638741 |
Fig. 2Frequency distribution of GRH nymph mortality after feeding on plants of the BC1F1 population derived from a cross between T65 (recurrent parent) and IRGC105715.
Quantitative trait loci (QTL) affecting resistance to green rice leafhopper in the BC1F1 population derived from a cross between ‘Taichung 65’ and IRGC105715
| QTL | Chromosome | Marker interval | Composite interval mapping | ||
|---|---|---|---|---|---|
|
| |||||
| Peak LOD score | PEV (%) | Additive effect | |||
| 4 | RM8213–RM5687 | 14.1 | 67.6 | −53.5 | |
| 7 | RM5405–RM3691 | 1.9 | 4.8 | −11.9 | |
| 12 | RM1261–RM1246 | 2.1 | 5.1 | −12.5 | |
Critical threshold value of the LOD score was equivalent to 3.5 at an experiment-wise significance level of 0.05.
Percentage of explained phenotypic variation.
The value indicates the effect of the Taichung 65 allele.
Fig. 3Frequency distribution of GRH nymph mortality after feeding on plants of the BC3F2 population derived from a cross between T65 and IRGC105715.
Fig. 4Linkage map around GRH6 on chromosome 4. (A) A linkage map constructed using 185 BC3F2 plants derived from a cross between ‘Taichung 65’ and IRGC105715. Vertical bars indicate the positions of SSR markers, and numbers between markers indicate genetic distance. (B) A high-resolution linkage map constructed using 6834 BC3F3 plants. Vertical bars indicate the positions of SSR markers, and numbers in parentheses indicate the number of recombination events. The pictured homozygous lines were selected from the progeny of these recombinants. Horizontal bars: white, homozygous for T65 chromosome segment; black, homozygous for IRGC105715 chromosome segment; gray, regions where recombination events occurred. The size of the candidate region of GRH6 is based on the IRGC105715 genome sequence. The asterisk and n.s. are significantly different from that of Line 6-1 at P = 0.001 and no significance according to Dunnett’s test, respectively.
Predicted genes in the candidate region of GRH6
| Gene ID in RAP-DB | Gene annotation in RAP-DB | Gene locus in MSU | Gene annotation in MSU | Predicted transcript size (bp) |
|---|---|---|---|---|
| Cysteine synthase (EC 2.5.1.47) | Cysteine synthase, chloroplast/chromoplast precursor, putative | 1435 | ||
| Hypothetical protein | – | – | 461 | |
| Conserved hypothetical protein | Leucine Rich Repeat family protein | 1869 | ||
| Conserved hypothetical protein | Leucine Rich Repeat family protein | 3653 |