The use of molecular markers is one of the most sensitive, powerful technologies for genetic purity assessment of seed lots. In this study, we aimed to develop a set of insertion and deletion (InDel) markers, through bioinformatics approaches, that may effectively distinguish three representative japonica rice (Oryza sativa L.) varieties, Nipponbare, Taichung 65 and Zhonghua11. The published whole-genome sequences of these varieties were aligned using BWA-MEM, followed by manual inspection for InDels of more than ten base pairs in size with the tview function of SAMtools. A set of ten InDel markers were thus identified and then validated by PCR in the three japonica rice varieties and their intercross F1 hybrids. Results showed that the InDel markers developed in this study could reliably distinguish these three japonica rice varieties. These molecular markers together with the detection method developed here can be applied to DNA-based genetic purity evaluation in rice breeding.

The complete chloroplast (cp) genome sequences of three Amaranthus species (Amaranthus hypochondriacus, A. cruentus and A. caudatus) were determined by next-generation sequencing. The cp genome sequences of A. hypochondriacus, A. cruentus and A. caudatus were 150,523, 150,757 and 150,523 bp in length, respectively, each containing 84 genes with identical contents and orders. Expansion or contraction of the inverted repeat region was not observed among the three Amaranthus species. The coding regions were highly conserved with 99.3% homology in nucleotide and amino acid sequences. Five genes – matK, accD, ndhJ, ccsA and ndhF – showed relatively high non-synonymous/synonymous values (Ka/Ks > 0.1). Sequence comparison identified two insertion/deletion (InDels) greater than 40 bp in length, and polymerase chain reaction markers that could amplify these InDel regions were applied to diverse Korean Genbank accessions, which could discriminate the three Amaranthus species. Phylogenetic analyses based on 62 protein-coding genes showed that the core Caryophyllales were monophyletic and Amaranthoideae formed a sister group with the Betoideae and Chenopodioideae clade. Comparing each homologous locus among the three Amaranthus species, identified eight regions with high Pi values (>0.03). Seven of these loci, except for rps19-trnH (GUG), were considered to be useful molecular markers for further phylogenetic studies.

About 40% of the global arable land is acidic, and in India, majority of these acidic soils are in the north-eastern region. Soil acidity leads to high phosphorus (P) fixation that causes P deficiency; therefore, there is a need to characterize the identified potential donors for acidic soils for P-deficiency tolerance. We evaluated rice genotypes for nucleotide variation in two loci reported for low P tolerance, namely PSTOL1 and PupK20-2. Sequence comparison for PSTOL1 revealed two distinct haplotypes. Genotypes with higher P uptake such as LR 19 and LR 23 had the desired Kasalath-type haplotype, whereas those with lower P uptake such as UR 29 and LR 39 showed a mixed haplotype. A total of four novel nucleotide variations were observed in 3′-UTR (untranslated region). Sequencing of PupK20-2 revealed a total of 28 SNPs and one insertion–deletion, of which 24 SNPs were novel. The discovery of novel SNPs across both PSTOL1 and PupK20-2 suggests the existence of novel haplotypes in genotypes adapted to acidic soil conditions. We reported for the first time the characterization of the donors being used in breeding programmes for acidic soils at the molecular level. The implications in breeding programmes are discussed.