Updating the elite rice variety Kongyu 131 by improving the Gn1a locus

Feng, Xiaoqin; Wang, Chen; Nan, Jianzong; Zhang, Xiaohui; Wang, Rongsheng; Jiang, Guoqiang; Yuan, Qingbo; Lin, Shaoyang

doi:10.1186/s12284-017-0174-1

Cited by 33 publications

(26 citation statements)

References 37 publications

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“…In previous reports, the Gn1a Habataki (type 3) allele significantly increased GNPP by 21% and 28~37% in temperate japonica cultivar (Koshihikari and Sasanishiki) backgrounds, respectively 13 , 15 . In addition, the Gn1a -indica allele increased grain yield in Kongyu 131 27 with elite japonica background. However, in our study, the Gn1a -type 3 allele derived from lines Habataki, ST12, and ST6 was not effective in several indica cultivar backgrounds that had the Gn1a -type 2 allele.…”

Section: Discussionmentioning

confidence: 97%

Introgression of a functional epigenetic OsSPL14WFP allele into elite indica rice genomes greatly improved panicle traits and grain yield

Kim

Ramos

Hizon

et al. 2018

Sci Rep

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Rice yield potential has been stagnant since the Green Revolution in the late 1960s, especially in tropical rice cultivars. We evaluated the effect of two major genes that regulate grain number, Gn1a/OsCKX2 and IPA1/WFP/OsSPL14, in elite indica cultivar backgrounds. The yield-positive Gn1a-type 3 and OsSPL14WFP alleles were introgressed respectively through marker-assisted selection (MAS). The grain numbers per panicle (GNPP) were compared between the recipient allele and the donor allele groups using segregating plants in BC3F2 and BC3F3 generations. There was no significant difference in GNPP between the two Gn1a alleles, suggesting that the Gn1a-type 3 allele was not effective in indica cultivars. However, the OsSPL14WFP allele dramatically increased GNPP by 10.6–59.3% in all four different backgrounds across cropping seasons and generations, indicating that this allele provides strong genetic gain to elite indica cultivars. Eventually, five high-yielding breeding lines were bred using the OsSPL14WFP allele by MAS with a conventional breeding approach that showed increased grain yield by 28.4–83.5% (7.87–12.89 t/ha) vis-à-vis the recipient cultivars and exhibited higher yield (~64.7%) than the top-yielding check cultivar, IRRI 156 (7.82 t/ha). We demonstrated a strong possibility to increase the genetic yield potential of indica rice varieties through allele mining and its application.

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Section: Discussionmentioning

confidence: 97%

Introgression of a functional epigenetic OsSPL14WFP allele into elite indica rice genomes greatly improved panicle traits and grain yield

Kim

Ramos

Hizon

et al. 2018

Sci Rep

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“…However, limited research has been focused on the MAS of yield-related traits in recent decades. Recently, beneficial alleles of the GS3 , Gn1a , and Hd1 genes were introgressed into Kongyu131, a high-quality cultivar widely planted in the northeastern region of China, which improved both the grain yield and regional adaptation of the newly developed lines (Feng et al 2017 ; Nan et al 2018 ; Wang et al 2019 ). To date, many gene-linked markers have been developed to facilitate MAS breeding but these gene-linked markers are not associated with the target alleles for the genes and can only be used for allele mining after their association with the target allele is confirmed (Hu et al 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice

Zhang

Bian

et al. 2020

Rice

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Background Grain size is an extremely important aspect of rice breeding, affecting both grain yield and quality traits. It is controlled by multiple genes and tracking these genes in breeding schemes should expedite selection of lines with superior grain yield and quality, thus it is essential to develop robust, efficient markers. Result In this study, 14 genes related to grain size (GW2, GS2, qLGY3, GS3, GL3.1, TGW3, GS5, GW5, GS6, TGW6, GW6a, GLW7, GL7 and GW8) were selected for functional marker development. Twenty-one PCR-gel-based markers were developed to genotype the candidate functional nucleotide polymorphisms (FNPs) of these genes, and all markers can effectively recognize the corresponding allele types. To test the allele effects of different FNPs, a global collection of rice cultivars including 257 accessions from the Rice Diversity Panel 1 was used for allele mining, and four grain-size-related traits were investigated at two planting locations. Three FNPs for GW2, GS2 and GL3.1 were genotyped as rare alleles only found in cultivars with notably large grains, and the allele contributions of the remaining FNPs were clarified in both the indica and japonica subspecies. Significant trait contributions were found for most of the FNPs, especially GS3, GW5 and GL7. Of note, GW5 could function as a key regulator to coordinate the performance of other grain size genes. The allele effects of several FNPs were also tested by QTL analysis using an F2 population, and GW5 was further identified as the major locus with the largest contribution to grain width and length to width ratio. Conclusions The functional markers are robust for genotyping different cultivars and may facilitate the rational design of grain size to achieve a balance between grain yield and quality in future rice breeding efforts.

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“…DNA extraction, PCR and high-resolution melting (HRM) analysis were carried out as described by Feng et al [14]. According to the physical position of the cloned blast resistance genes and the SNPs between Kongyu-131 and GKGH, 12 SNP markers tightly linked to corresponding blast resistance genes were developed to genotype the F 2 population.…”

Section: Methodsmentioning

confidence: 99%

“…By resequencing the genome of Kongyu-131 and comparing it with cloned R-gene sequences, Zhang et al found that Kongyu-131 lacked almost all the R-genes except for Pish [13]. By using the principle of genome updating described by Feng et al [14], we mined a favorable blast resistance gene module (a small chromosome segment hosting a superior pi21 allelic variant from a blast-resistant upland variety) to improve the blast resistance of Kongyu-131 in this study.…”

Section: Introductionmentioning

confidence: 99%

Improving the blast resistance of the elite rice variety Kongyu-131 by updating the pi21 locus

et al. 2019

Self Cite

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Background As an elite japonica rice variety, Kongyu-131 has been cultivated for over 20 years in the third accumulated temperature zone of Heilongjiang Province, China. However, the cultivated area of Kongyu-131 has decreased each year due to extensive outbreaks of rice blast. To achieve the goals of improving blast resistance and preserving other desirable traits in Kongyu-131, a genome-updating method similar to repairing a bug in a computer program was adopted in this study. A new allele of the broad-spectrum blast resistance gene pi21 in the upland rice variety GKGH was mined by genetic analysis and introgressed into the genome of Kongyu-131 to upgrade its blast resistance. Result QTL analysis was performed with an F 2 population derived from a cross between Kongyu-131 and GKGH, and a blast resistance QTL was detected near the pi21 locus. Parental Pi21 sequence alignment showed that the pi21 of the donor (GKGH) was a new allele. By 5 InDel or SNP markers designed based on the sequence within and around pi21 , the introgressed chromosome segment was shortened to less than 634 kb to minimize linkage drag by screening recombinants in the target region. The RRPG was 99.92%, calculated according to 201 SNP markers evenly distributed on 12 chromosomes. Artificial inoculation at the seedling stage showed that the blast resistance of the new Kongyu-131 was improved significantly. Field experiments also indicated that the improved Kongyu-131 had enhanced field resistance to rice blast and grain-quality traits similar to those of the original Kongyu-131. Conclusions It is feasible to improve resistance to rice blast and preserve other desirable traits by precisely improving the Pi21 locus of Kongyu-131. Linkage drag can be eliminated effectively via recombinant selection on both sides of the target gene.

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Updating the elite rice variety Kongyu 131 by improving the Gn1a locus

Cited by 33 publications

References 37 publications

Introgression of a functional epigenetic OsSPL14WFP allele into elite indica rice genomes greatly improved panicle traits and grain yield

Introgression of a functional epigenetic OsSPL14WFP allele into elite indica rice genomes greatly improved panicle traits and grain yield

Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice

Improving the blast resistance of the elite rice variety Kongyu-131 by updating the pi21 locus

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