Waxy gene haplotypes: Associations with apparent amylose content and the effect by the environment in an international rice germplasm collection

Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome

Background

The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers.

Methodology/Principal Findings

In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations.

Conclusions/Significance

Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.

Development of genome-specific primers for homoeologous genes in allopolyploid species: the waxy and starch synthase II genes in allohexaploid wheat (Triticum aestivum L.) as examples

BACKGROUND

In allopolypoid crops, homoeologous genes in different genomes exhibit a very high sequence similarity, especially in the coding regions of genes. This makes it difficult to design genome-specific primers to amplify individual genes from different genomes. Development of genome-specific primers for agronomically important genes in allopolypoid crops is very important and useful not only for the study of sequence diversity and association mapping of genes in natural populations, but also for the development of gene-based functional markers for marker-assisted breeding. Here we report on a useful approach for the development of genome-specific primers in allohexaploid wheat.

FINDINGS

In the present study, three genome-specific primer sets for the waxy (Wx) genes and four genome-specific primer sets for the starch synthase II (SSII) genes were developed mainly from single nucleotide polymorphisms (SNPs) and/or insertions or deletions (Indels) in introns and intron-exon junctions. The size of a single PCR product ranged from 750 bp to 1657 bp. The total length of amplified PCR products by these genome-specific primer sets accounted for 72.6%-87.0% of the Wx genes and 59.5%-61.6% of the SSII genes. Five genome-specific primer sets for the Wx genes (one for Wx-7A, three for Wx-4A and one for Wx-7D) could distinguish the wild type wheat and partial waxy wheat lines. These genome-specific primer sets for the Wx and SSII genes produced amplifications in hexaploid wheat, cultivated durum wheat, and Aegilops tauschii accessions, but failed to generate amplification in the majority of wild diploid and tetraploid accessions.

CONCLUSIONS

For the first time, we report on the development of genome-specific primers from three homoeologous Wx and SSII genes covering the majority of the genes in allohexaploid wheat. These genome-specific primers are being used for the study of sequence diversity and association mapping of the three homoeologous Wx and SSII genes in natural populations of both hexaploid wheat and cultivated tetraploid wheat. The strategies used in this paper can be used to develop genome-specific primers for homoeologous genes in any allopolypoid species. They may be also suitable for (i) the development of gene-specific primers for duplicated paralogous genes in any diploid species, and (ii) the development of allele-specific primers at the same gene locus.

An efficient computational method for screening functional SNPs in plants

Granule Bound Starch Synthase I (GBSSI), which influences the grain quality of cereals and, particularly, rice, is one of the most important plant genes. Using GBSSI as a model plant gene in this study, we examined a number of different computational algorithm tools and programs to explore the functional SNPs of this important rice gene and the possible relationships between genetic mutation and phenotypic variation. A total of 51 SNPs/indels were retrieved from databases, including three important coding non-synonymous SNPs, namely those in exons 6, 9 and 10. Sorting Intolerant from Tolerant (SIFT) results showed that a candidate [C/A] SNP (ID: OryzaSNP2) in exon 6 (coordinate 2494) is the most important non-synonymous SNP with the highest phenotypic impact on waxy protein. This SNP can alter a tyrosine to serine residue at position 224 of waxy protein. Computational simulation of GBSSI protein with the Geno3D suggested that this mutant SNP creates a bigger loop on the surface of waxy protein and results in a shape different from that of native GBSSI. Here, we suggest a potential transcriptional binding factor site (TBF8) which has one [C/T] SNP [rs53176842] at coordinate 2777 in boundary site of intron 7/exon 8, according to Transcriptional Factor (TF) search analysis. This SNP might potentially have a major effect on regulation and function of GBSSI. Combining SNP mining data and in silico structural analysis of waxy protein led us to prepare an efficient computational pathway which can be applied for other plant genes.

Identification and characterization of a novel Waxy allele from a Yunnan rice landrace

Low amylose content (AC) is a desirable trait for rice (Oryza sativa L.) cooking quality and is selected in soft rice breeding. To gain a better understanding of the molecular mechanism controlling AC formation, we screened 83 Yunnan rice landraces in China and identified a rice variety, Haopi, with low AC. Genetic analyses and transgenic experiments revealed that low AC in Haopi was controlled by a novel allele of the Wx locus, Wx(hp), encoding a granule-bound starch synthase (GBSSI). Sequence comparisons of Wx(hp) and Wx(b) alleles (from Nipponbare) showed several nucleotide changes in the upstream regulatory regions (including the promoter, 5'-untranslated region, and first intron 5' splicing junction site). Interestingly, these changes had no obvious effect on the expression level and splicing efficiency of Wx transcripts. In addition, an examination of the coding region revealed that the Wx(hp) allele carries an A-to-G change at nucleotide position +497 from the start codon, resulting in an Asp(165)/Gly(165) substitution. The amino acid substitution had no detectable effects on GBSSI activity in vitro; however, it notably reduced the binding of GBSSI to starch granules, resulting in a reduction of AC in rice seeds. Moreover, three other Yunnan landraces with low AC also carry a nucleotide substitution identical to Haopi at the +497 position of the Wx gene, suggesting common ancestry. Based on the single-nucleotide polymorphism, we have developed a new derived cleaved amplified polymorphic sequence marker for use in breeding practice to manipulate AC in rice endosperm.

Not just a grain of rice: the quest for quality

A better understanding of the factors that contribute to the overall grain quality of rice (Oryza sativa) will lay the foundation for developing new breeding and selection strategies for combining high quality, with high yield. This is necessary to meet the growing global demand for high quality rice while offering producing countries additional opportunities for generating higher export revenues. Several recent developments in genetics, genomics, metabolomics and phenomics are enhancing our understanding of the pathways that determine several quality traits. New research strategies, as well as access to the draft of the rice genome, will not only advance our understanding of the molecular mechanisms that lead to quality rice but will also pave the way for efficient and targeted grain improvement.