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SNP Discovery and Genetic Variation of Candidate Genes Relevant to Heat Tolerance and Agronomic Traits in Natural Populations of Sand Rice ( Agriophyllum squarrosum )

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ABSTRACT

The extreme stress tolerance and high nutritional value of sand rice (Agriophyllum squarrosum) make it attractive for use as an alternative crop in response to concerns about ongoing climate change and future food security. However, a lack of genetic information hinders understanding of the mechanisms underpinning the morphological and physiological adaptations of sand rice. In the present study, we sequenced and analyzed the transcriptomes of two individuals representing semi-arid [Naiman (NM)] and arid [Shapotou (SPT)] sand rice genotypes. A total of 105,868 pairwise single nucleotide polymorphisms (SNPs) distributed in 24,712 Unigenes were identified among SPT and NM samples; the average SNP frequency was 0.3% (one SNP per 333 base pair). Characterization of gene annotation demonstrated that variations in genes involved in DNA recombination were associated with the survival of the NM population in the semi-arid environment. A set of genes predicted to be relevant to heat stress response and agronomic traits was functionally annotated using the accumulated knowledge from Arabidopsis and several crop plants, including rice, barley, maize, and sorghum. Four candidate genes related to heat tolerance (heat-shock transcription factor, HsfA1d), seed size (DA1-Related, DAR1), and flowering (early flowering 3, ELF3 and late elongated hypocotyl, LHY) were subjected to analysis of the genetic diversity in 10 natural populations, representing the core germplasm resource across the area of sand rice distribution in China. Only one SNP was detected in each of HsfA1d and DAR1, among 60 genotypes, with two in ELF3 and four in LHY. Nucleotide diversity ranged from 0.00032 to 0.00118. Haplotype analysis indicated that the NM population carried a specific allele for all four genes, suggesting that divergence has occurred between NM and other populations. These four genes could be further analyzed to determine whether they are associated with phenotype variation and identify alleles favorable for sand rice breeding.

No MeSH data available.


Boxplot of pairwise sand rice SNP frequencies in each of the SNP defined Unigene categories described in Figure 4.
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Figure 5: Boxplot of pairwise sand rice SNP frequencies in each of the SNP defined Unigene categories described in Figure 4.

Mentions: Single nucleotide polymorphism distribution and frequency are important indices for genome wide SNP development. In this study, all pairwise SNPs were distributed in 24,712 of 91,884 reference Unigenes, with approximately 57% (14,130) containing fewer than three SNPs (Figure 4A). A histogram of SNP frequency revealed a peak at 0.2 and 61.24% Unigenes were under the average SNP frequency of 0.3% (Figure 4B). Among the 24,712 Unigenes, 22,538 contained inter-individual SNPs, and 1,534 and 9,278 contained NM- and SPT-specific SNPs, respectively (Figure 4C). There were 16,756 Unigenes containing only one type of SNP, while 682 had all three types. Categories were named according to the gene number in each set in the Venn diagram (Figure 5). The mean SNP frequency values for all categories were lower than 0.45%; however, the four categories (SR_682, SR_6614, SR_465, and SR_195) including two or three types of SNP, exhibited higher frequencies than the other categories (p < 0.01; Figure 5). Detailed histograms illustrating SNP numbers and frequencies for each category are presented in Supplementary Figure 3.


SNP Discovery and Genetic Variation of Candidate Genes Relevant to Heat Tolerance and Agronomic Traits in Natural Populations of Sand Rice ( Agriophyllum squarrosum )
Boxplot of pairwise sand rice SNP frequencies in each of the SNP defined Unigene categories described in Figure 4.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5383723&req=5

Figure 5: Boxplot of pairwise sand rice SNP frequencies in each of the SNP defined Unigene categories described in Figure 4.
Mentions: Single nucleotide polymorphism distribution and frequency are important indices for genome wide SNP development. In this study, all pairwise SNPs were distributed in 24,712 of 91,884 reference Unigenes, with approximately 57% (14,130) containing fewer than three SNPs (Figure 4A). A histogram of SNP frequency revealed a peak at 0.2 and 61.24% Unigenes were under the average SNP frequency of 0.3% (Figure 4B). Among the 24,712 Unigenes, 22,538 contained inter-individual SNPs, and 1,534 and 9,278 contained NM- and SPT-specific SNPs, respectively (Figure 4C). There were 16,756 Unigenes containing only one type of SNP, while 682 had all three types. Categories were named according to the gene number in each set in the Venn diagram (Figure 5). The mean SNP frequency values for all categories were lower than 0.45%; however, the four categories (SR_682, SR_6614, SR_465, and SR_195) including two or three types of SNP, exhibited higher frequencies than the other categories (p < 0.01; Figure 5). Detailed histograms illustrating SNP numbers and frequencies for each category are presented in Supplementary Figure 3.

View Article: PubMed Central - PubMed

ABSTRACT

The extreme stress tolerance and high nutritional value of sand rice (Agriophyllum squarrosum) make it attractive for use as an alternative crop in response to concerns about ongoing climate change and future food security. However, a lack of genetic information hinders understanding of the mechanisms underpinning the morphological and physiological adaptations of sand rice. In the present study, we sequenced and analyzed the transcriptomes of two individuals representing semi-arid [Naiman (NM)] and arid [Shapotou (SPT)] sand rice genotypes. A total of 105,868 pairwise single nucleotide polymorphisms (SNPs) distributed in 24,712 Unigenes were identified among SPT and NM samples; the average SNP frequency was 0.3% (one SNP per 333 base pair). Characterization of gene annotation demonstrated that variations in genes involved in DNA recombination were associated with the survival of the NM population in the semi-arid environment. A set of genes predicted to be relevant to heat stress response and agronomic traits was functionally annotated using the accumulated knowledge from Arabidopsis and several crop plants, including rice, barley, maize, and sorghum. Four candidate genes related to heat tolerance (heat-shock transcription factor, HsfA1d), seed size (DA1-Related, DAR1), and flowering (early flowering 3, ELF3 and late elongated hypocotyl, LHY) were subjected to analysis of the genetic diversity in 10 natural populations, representing the core germplasm resource across the area of sand rice distribution in China. Only one SNP was detected in each of HsfA1d and DAR1, among 60 genotypes, with two in ELF3 and four in LHY. Nucleotide diversity ranged from 0.00032 to 0.00118. Haplotype analysis indicated that the NM population carried a specific allele for all four genes, suggesting that divergence has occurred between NM and other populations. These four genes could be further analyzed to determine whether they are associated with phenotype variation and identify alleles favorable for sand rice breeding.

No MeSH data available.