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.

Sung-Ryul Kim,Kshirod K Jena,Ramil Mauleon,Sherry Lou Hechanova,Motoyuki Ashikari,Edgar A Torres,Eero Nissila,Joie Ramos,Parminder S Virk

doi:10.1186/s12284-016-0084-7

Sung-Ryul Kim, Kshirod K Jena + Show 7 more

Open Access

https://doi.org/10.1186/s12284-016-0084-7

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Abstract

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.

Highlights

Rice is one of the major staple foods in the world, especially in the developing countries of Asia
Development of allele-specific markers for eight yieldenhancing genes was conducted as a part of our breeding program for increasing genetic yield potential in 12 elite indica varietal backgrounds (Table 1)
For determination of alleles of yield-enhancing genes in 12 recipient cultivars and effective screening of polymorphisms between the donor and the recipient, we sequenced the whole genomes of three donors (Habataki, ST6, and ST12) and three recipients (NSIC Rc158, NSIC Rc222, and NSIC Rc238) using next-generation sequencing technique

Summary

Introduction

Rice is one of the major staple foods in the world, especially in the developing countries of Asia. Three major traits (grain size, grain number per panicle, and panicle number per plant) are directly associated with rice grain productivity, and these traits strongly depend on the genetic potential of rice. These traits are complex and quantitative in nature. The loss of GW2 function by a premature stop codon caused by a 1-bp deletion on the fourth exon increased grain width, resulting in increased yield (Song et al 2007). The nucleotide substitution from C to A on the second exon resulted in the stop codon (TGA) and eventually caused C-terminal truncated GS3 protein This mutated allele increased grain size (Fan et al 2006). The mutant allele (1-bp deletion in CDS) showed increased thousand-grain weight (Ishimaru et al 2013)

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