InDel marker based genetic differentiation and genetic diversity in traditional rice (Oryza sativa L.) landraces of Chhattisgarh, India

Abstract

Rice has been cultivating and utilizing by humans for thousands of years under diverse environmental conditions. Therefore, tremendous genetic differentiation and diversity has occurred at various agro-ecosystems. The significant indica–japonica differentiation in rice provides great opportunities for its genetic improvement. In the present investigation, a total of 42 polymorphic InDel markers were used for differentiating 188 rice landraces and two local varieties of Chhattisgarh, India into indica and japonica related genotypes based on ‘InDel molecular index’. Frequency of japonica alleles varied from 0.11 to 0.89 among landraces. Results revealed that 104 rice landraces have indica type genetic architecture along with three tested indica cultivars Swarna, Mahamaya and Rajeshwari. Another 60 landraces were placed under ‘close to indica’ type. It was found that three rice landraces i.e. Kalajeera, Kapri, Tulsimala were ‘close to japonica’ type and 21 landraces were ‘intermediate’ type. The result from the calculation of ‘InDel molecular index’ was further verified with STRUCTURE, AMOVA, PCA and cluster analysis. Population structure analysis revealed two genetically distinct populations within the 190 rice landraces/genotypes. Based on AMOVA, ‘intermediate’ type, ‘close to japonica’ type and Dongjinbyeo (a japonica cultivar from Republic of Korea) displayed significant genetic differentiation (ɸPT = 0.642, P = 0.000) from ‘indica’ and ‘close to indica’ groups. The PCA scatter plot and dendrogram demonstrated a clear pattern of two major group differentiations. ‘Close to japonica’ type and ‘intermediate’ type landraces/genotypes were grouped with Dongjinbyeo and formed a separate cluster at 30% Jaccard’s similarity level from rest of the landraces/genotypes which were ‘close to indica’ or ‘indica’ type. Such a significant genetic differentiation among the locally adapted landraces could be exploited for the development of rice varieties introgressing higher yield potential and better plant types of japonica type as per the need of consumers and rice traders.

Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species

“…The two O. sativa subspecies, indica and japonica , are also taxonomically classified based on their morphological traits (number of tillers, plant height, plant type, plant pubescence, and type/length of grains) in combination with other traits (including winter hardiness, starch types and phenol response in grains) 6 . However, the phenotypic attributes used to differentiate indica from japonica have low resolution to clearly separate many collections, are laborious to measure and are highly affected by environmental conditions.…”

“…However, the phenotypic attributes used to differentiate indica from japonica have low resolution to clearly separate many collections, are laborious to measure and are highly affected by environmental conditions. Since the advent of molecular marker technology, the phylogenetic relationships among the Oryza species have been determined using both low-density and high-density molecular markers 1 , 6 – 8 . Recently, our team at the AfricaRice reported 339 diagnostic single nucleotide polymorphic (SNP) markers that can be used for accurate taxonomic classification of the O. barthii, O. glaberrima , O. longistaminata and the two O. sativa subspecies 5 , 9 .…”

Development and Application of Novel InDel Markers in Flax (Linum usitatissimum L.) Through Whole-Genome Re-Sequencing

“…Owing to the low cost and high e ciency of sequencing, InDel can be developed easily using high-throughput sequencing [27,28]. InDel markers have been used in rice [29][30][31], jute [32], quinoa [33], cabbage [25], cucumber [34], tomato [35] and other crops [26,28,[36][37][38], and are mainly used for germplasm resource identi cation, genetic diversity analysis, and genetic map construction. However, there are no reports available on the development and application of InDel markers in ax.…”

Whole-genome sequencing of three local rice varieties (Oryza sativa L.) in Vietnam

“…Compared to the need for unique facilities for SNP detection (6), the codominant technology for InDels is user-friendly and beneficial in some genetic analyses, especially in marker-assisted selection (MAS) (7). With the advancement of NGS technology and cost reduction, InDels were widely detected and created HORIZON e-Publishing Group via resequencing and became a precious resource for the research of many organisms, especially rice (8,9). This study aimed to detect and create stable and practical InDel markers based on information resequencing from three closely related rice lines, NTCD-T (aroma), NTCD-TN (mild aroma), and Tai Nguyen, compared to a reference genome sequence, Nipponbare, so that the NTCD-T national rice cultivar can be authenticable and distinguished from other Vietnamese rice cultivars.…”