Breeding value estimation of the application of IPA1 and DEP1 to improvement of Oryza sativa L. ssp. japonica in early hybrid generations

Xu, Quan; Xu, Na; Xu, Hai Jun; Tang, Liang; Li, Jin; Sun, Jian; Wang, Jiayu

doi:10.1007/s11032-014-0150-z

Cited by 19 publications

(14 citation statements)

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“…The Di value reflected the variation caused by random genetic backgrounds rather than the regulatory genes, its influences on MRW, C and HR need to be deeply discussed. Many studies had proved that gene contribution rates differ depending on their genetic backgrounds (Huang et al 2009;Xu et al 2014), and the genetic backgrounds' random introduction from indica may also contain the other QTLs that not be successfully cloned (Ren et al 2016). We speculated that the variations containing genetic backgrounds and multiple QTLs all contributed to its influences on MRW, C and HR.…”

Section: Discussionmentioning

confidence: 98%

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Discussion on strategy of grain quality improvement for super high yielding japonica rice in Northeast China

Mei

Jiang³

et al. 2017

Journal of Integrative Agriculture

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japonica rice is mainly distributed in Northeast China and accounts for 44.6% of the total cultivated area of japonica rice in China. The comprehensive using of inter-subspecies heterosis is the main breeding mode of super japonica rice varieties in this region. Improving rice quality at relative high yielding level is the current research focus. Performing crosses between indica and japonica lines allows for the recombination of regulatory genes and genetic backgrounds, leading to complicated genetic rice quality characteristics, which can be used to explore patterns of quality improvement. In the present study, we utilize recombinant inbred lines (RILs) derived from indica-japonica hybridization to analyze the effect factors of rice quality derived from genetic factors, which contain both regulatory genes concerning rice quality and genetic backgrounds' random introduction frequency coming from indica (Di value), and the improvement strategy was further discussed. The regulatory genes involved in amylase content (Wx) and nitrogen utilization efficiency (NRT1.1B) were the major factors affecting the amylose content (AC) and protein content (PC) in RILs, respectively. Both the Di value and the major grain width gene (GS5) had regulatory effects on milled rice width (MRW) in RILs, and their interaction explained the major variance of MRW in the RILs. With the mediation of MRW and chalkiness degree (C), Di value had a further impact on head rice rate (HR), which was relatively poor when the Di value was over 40%. In Northeast China, the Di value should be lowered by backcrossing or multiple crosses during the breeding of indica-japonica hybridization to maintain the whole better HR and further to emphasize the use of favorable genes in individual selection.

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Section: Discussionmentioning

confidence: 98%

“…The majority of loci affecting rice quality are QTLs, and the differences in their explained phenotypic variation were relatively great under different genetic backgrounds (Cui et al 2003;Huang et al 2009;Xu et al 2014). Additionally, the number of confirmed regulatory genes is extremely limited.…”

Section: Introductionmentioning

confidence: 99%

Discussion on strategy of grain quality improvement for super high yielding japonica rice in Northeast China

Mei

Jiang³

et al. 2017

Journal of Integrative Agriculture

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“…Yan et al ( 2009 ) developed the Gn1a-M1 marker for the detection of Gn1a -Habataki allele, which has a 16-bp deletion in the 5’-untranslated region (5’UTR), and the Gn1a-M2 marker for the detection of Gn1a -5150 allele, which has an 11-bp deletion on the third exon. Xu et al ( 2014 ) developed the CAPS marker using Sdu I restriction enzyme to select OsSPL14 -Ri22 allele, which transcribes OsmiR156-resistant OsSPL14 transcripts caused by the nucleotide substitution at the OsmiR156 target site. They also developed the gene-tagged PCR marker of DEP1 gene using the 625-bp gap on the fifth exon between the yield-positive allele and non-target allele.…”

Section: Introductionmentioning

confidence: 99%

“…For the Gn1a gene, a 16-bp deletion in 5’UTR is common in indica rice varieties (54.3%) (Yan et al 2009 ), suggesting that the Gn1a -M1 marker may not function in many indica varieties. For the DEP1 marker (Xu et al 2014 ), the intensity of the non-target allele band was very weak compared with that of the target allele in the heterozygous plants. To obtain clear genotype data, the previous DEP1 marker needs to be improved.…”

Section: Introductionmentioning

confidence: 99%

Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

Kim

Ramos

Ashikari

et al. 2016

Rice

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BackgroundRice is one of the major staple foods in the world, especially in the developing countries of Asia. Its consumption as a dietary source is also increasing in Africa. To meet the demand for rice to feed the increasing human population, increasing rice yield is essential. Improving the genetic yield potential of rice is one ideal solution. It is imperative to introduce the identified yield-enhancing gene(s) into modern rice cultivars for the rapid improvement of yield potential through marker-assisted breeding.ResultsWe report the development of PCR-gel-based markers for eight yield-related functional genes (Gn1a, OsSPL14, SCM2, Ghd7, DEP1, SPIKE, GS5, and TGW6) to introduce yield-positive alleles from the donor lines. Six rice cultivars, including three each of donor and recipient lines, respectively, were sequenced by next-generation whole-genome sequencing to detect DNA polymorphisms between the genotypes. Additionally, PCR products containing functional nucleotide polymorphism (FNP) or putative FNPs for yield-related genes were sequenced. DNA polymorphisms discriminating yield-positive alleles and non-target alleles for each gene were selected through sequence analysis and the allele-specific PCR-gel-based markers were developed. The markers were validated with our intermediate breeding lines produced from crosses between the donors and 12 elite indica rice cultivars as recipients. Automated capillary electrophoresis was tested and fluorescence-labeled SNP genotyping markers (Fluidigm SNP genotyping platform) for Gn1a, OsSPL14, Ghd7, GS5, and GS3 genes were developed for high-throughput genotyping.ConclusionsThe SNP/indel markers linked to yield related genes functioned properly in our marker-assisted breeding program with identified high yield potential lines. These markers can be utilized in local favorite rice cultivars for yield enhancement. The marker designing strategy using both next generation sequencing and Sanger sequencing methods can be used for suitable marker development of other genes associated with useful agronomic traits.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0084-7) contains supplementary material, which is available to authorized users.

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“…The indica allele frequency was calculated as the ratio of the number of indicatype markers to the total number of markers. The DEP1 locus was genotyped as described previously (Xu et al 2014). …”

Section: Dna Extraction and Subspecies-specific Genotypingmentioning

confidence: 99%

Different effects of DEP1 on vascular bundle- and panicle-related traits under indica and japonica genetic backgrounds

Liu

et al. 2015

Mol Breeding

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Rice (Oryza sativa L.) is a major food for more than half of the world's population and serves as a model monocot plant. DEP1 (dense and erect panicle 1), corresponding to an erect-panicle architecture, may bring the third breakthrough in rice breeding after the introduction of the semi-dwarf trait and the application of heterosis in hybrid rice. The aim of this study was to determine the effects of DEP1 on yield components and vascular bundle-related traits under indica and japonica genetic backgrounds. We analyzed a series of recombinant inbred lines, which were derived from a cross between the japonica variety SN265 with an erect panicle and the indica variety R99 with a curved panicle. The results showed that effects of the DEP1/dep1 allele were much stronger than the effects of the indica/japonica genetic background on vascular bundle-related traits and yield components. As the frequency of indica alleles increased, the grain yield per plant and the harvest index significantly increased in lines with the dep1 allele. Among the indica-type lines, those with the dep1 allele showed superior values for almost all of the vascular bundle-related traits and yield components. Our results provide new insights into the use of a highyield-related gene derived from japonica in the indica genetic background. have contributed equally to this work.Electronic supplementary material The online version of this article (

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Breeding value estimation of the application of IPA1 and DEP1 to improvement of Oryza sativa L. ssp. japonica in early hybrid generations

Cited by 19 publications

References 19 publications

Discussion on strategy of grain quality improvement for super high yielding japonica rice in Northeast China

Discussion on strategy of grain quality improvement for super high yielding japonica rice in Northeast China

Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

Different effects of DEP1 on vascular bundle- and panicle-related traits under indica and japonica genetic backgrounds

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