Assessment of diversity of Indian aromatic rice germplasm collections for morphological, agronomical, quality traits and molecular characters to identify a core set for crop improvement

Abstract

Background Besides the Basmati, the aromatic rice germplasm (ARG) accessions are treasured for quality, medicinal value and aroma. The demand for aromatic rice is ever increasing. Genetic diversity is the source of variability to identify superior alleles controlling morphological, agronomic and quality traits, and molecular attributes. This study reports on the characterization of traits in ARG to identify a core set for breeding high-yielding varieties. Methods The genetic diversity was measured on the distinctness, uniformity and stability (DUS) of 46 traits in 208 Indian ARG in field, greenhouse and laboratory tests. We performed individual and combined analysis of DUS traits and molecular data generated using 55 SSR markers. The genetic distances between genotypes were estimated using Mahalanobis D2 analysis and clustering by standardized Euclidean2 distances, Ward Minimum variance, Gowers’ similarity index and PowerMarker. The aim was to derive a core set of non-Basmati ARG using PowerCore to deploy in crop improvement. Results Eighty-two alleles were detected. Alleles per marker ranged from 2 (RM505) to 5 (RM276) with an average of 3.04 alleles. The markers are informative in analyzing the diversity as the PIC values estimated varied from 0.17 (RM577 on chromosome 1) to 0.72 (RM276 on chromosome 6) with an average of 0.54 per locus. RM276 with repeat motif of (AG)8A3(GA) 33 on chromosome 6 was the most informative (amplified 5 alleles). The combined analysis had shown genotypes in a few clusters to be more diverse than others. SSR markers RM289, RM505, RM577 and RM22866 were identified as genotype specific markers. With PowerCore, 46 genotypes (22%) were identified as a core set of ARG that represent all the alleles detected in the entire set investigated. 2-Acetyl-1-pyrroline is considered to impart aroma; it was not detected by GC–MS tests in many ARG. Conclusions Forty-six genotypes in the core set have different maturity periods, plant statures, grain types and grain quality traits. A parent can be selected from the core set to improve aromatic rice depending on the breeding objective. The olfactory sensing of strong aroma emitted by cooked kernels of all ARG was found more decisive than the costly GC–MS tests.

DNA Marker Based Diversity Across Rice Genotypes and Advanced Breeding Lines Bred for Temperate India

“…Similarly, Richa [26] grouped the genotypes into 4 major clusters based on UPGMA clustering method with Jaccard's similarity coe cient ranging from 0.38 to 0.92. Maliha, Exonam and Prasad [42][43][44] also reported the similar results.…”

Grain yield performance of hybrid rice in relation to inbred cultivars in long‐term multi‐environment tests in India

“…Two thousand and seventy hybrid F 1 genotypes in Initial Hybrid Rice Trials (IHRT) were evaluated in METs of AICIRP for 32 yr at 102 locations (ICAR-IIRR, 1968-2020. Many rice cultivars are grown under the irrigated ecosystem (>22 m ha -1 ) in monsoon-dependent India.…”

“…Fifty-four ILCvs were also planted in METs along with F 1 hybrid genotypes from 1988 and 2019 at 102 locations; ILCvs ranged from 12 to 23 in IHRT-E, from 9 to 27 in IHRT-ME, from 10 to 27 in IHRT-MED and from 1 to 5 in IHRT-MS trials. From the results presented by AICRIP for each trial over a period of 32 yr (ICAR-IIRR, 1968-2020, the mean annual yields of the T3HM were derived across all test sites. Similarly, ILCv mean yield ILCvM and EXPM yield estimated year-wise over locations were also derived and saved for later analysis (Supplemental Table S1, sheet 1).…”

“…In the dynamic hybrid rice-breeding program, hybrid genotypes with improvement in yields or in other traits of economic value, when compared with inbred local check cultivar (ILCv) are identified through phenotype-based selection and released for commercial cultivation. Each year hybrid F 1 genotypes with improvement in yields over ILCv are assessed by All India Coordinated Project (AICRIP) in nationally coordinated multi-environment tests (METs) in the irrigated ecosystem (ICAR-IIRR, 1968-2020. During their evaluation, yield, grain quality, and resistance to biotic and abiotic stresses are ranked.…”

Productivity and Profitability of Aromatic Rice Production in the Philippines

“…Its pandan-like scent translates to a higher price in the market compared to ordinary white rice (Bairagi, Demont, Custodio, & Ynion, 2020). With this quality attribute, consumer demand for aromatic rice has been generally increasing (Prasad, Padmavathi, & Suneetha, 2020) and is expected to expand more in the future (Prodhan & Qingyao, 2020). Rice farmers and traders from different parts of the world are also considering to enter this industry (Giraud, 2008).…”