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

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.

Evolution and functional differentiation of recently diverged phytochelatin synthase genes from Arundo donax L.

“…This level of divergence was higher than those usually observed among alleles of single genetic loci in plants (e.g. Brown et al , 2004; Tatarinova et al , 2016; Zhao et al , 2017). Phylogenetic analyses of the last intron of AdPCS1-3 isolated from four different Arundo species clearly showed that divergence among sequences predated the evolutionary split among species and ruled out recombination (Supplementary Fig.…”

Variations in Flavonoid Metabolites Along Altitudinal Gradient in a Desert Medicinal Plant Agriophyllum squarrosum

“…It is widely distributed in mobile sand and semi-fixed dunes across all the arid and semi-arid regions in Central Asia, the Caucasus, Mongolia, and Siberia, including the Qinghai-Tibet Plateau ( Wu et al, 2003 ). It can survive in extremely high temperatures and drought conditions and can tolerate sand burial ( Chen et al, 2014 ; Li et al, 2015 ; Zhao et al, 2017 ). Since the withered plants can reduce wind velocity by more than 90%, they also acted as nutrient providers and reservoirs with a rich source of carbon and nitrogen in infertile soil environments.…”

Morphological description and DNA barcoding study of sand rice (Agriophyllum squarrosum, Chenopodiaceae) collected in Kazakhstan

“…Physiology and morphology of sand rice are ideally adapted to the extreme desert conditions [ 13 ], which make A. squarrosum interesting for studying its genomic basis of xeric adaptations. In the last 10 years, there were several works dedicated to the search of candidate genes responsible for the tolerance to heat and drought stresses [ 14 ]. One of the current primary goals is the domestication of sand rice in desert environments [ 15 ] via development of plants with larger grains and higher yield, and to exclude unfavorable phenotypic traits such as seed shattering, thorns, etc.…”