Deciphering Genetics Underlying Stable Anaerobic Germination in Rice: Phenotyping, QTL Identification, and Interaction Analysis

Abstract

Anaerobic germination (AG) is an important trait for direct-seeded rice (DSR) to be successful. Rice usually has low germination under anaerobic conditions, which leads to a poor crop stand in DSR when rain occurs after seeding. The ability of rice to germinate under water reduces the risk of poor crop stand. Further, this allows the use of water as a method of weed control. The identification of the genetic factors leading to high anaerobic germination is required to develop improved DSR varieties. In the present study, two BC₁F_2:3 mapping families involving a common parent with anaerobic germination potential, Kalarata, an indica landrace, and two recurrent parents, NSIC Rc222 and NSIC Rc238, were used. Phenotyping was done under two environmental conditions and genotyping was carried out through the KASP SNP genotyping platform. A total of 185 and 189 individuals genotyped with 170 and 179 polymorphic SNPs were used for QTL analysis for the two populations, Kalarata/NSIC Rc238 and Kalarata/NSIC Rc222, respectively. A total of five QTLs on chromosomes 3, 5, 6, 7, and 8 for survival (SUR) and four QTLs on chromosomes 1, 3 (two locations), and 7 for the trait seedling height (SH) across the populations and over the screening conditions were identified. Except for the QTLs on chromosomes 5 and 8, the parent with AG potential, Kalarata, contributed all the other QTLs. Among the five QTLs for SUR, the second-largest QTL (qSUR6-1) was novel for AG potential in rice, showing a stable expression in terms of genetic background and screening conditions explaining 11.96% to 16.01% of the phenotypic variation. The QTL for SH (qSH1-1) was also novel. Considering different genetic backgrounds and different screening conditions, the QTLs identified for the trait SUR explained phenotypic variation in the range of 57.60% to 73.09% while that for the trait SH ranged from 13.53% to 34.30%.

Keywords: Anaerobic germination; KASP; QTLs; Rice; SNPs.

Fig. 1

Phenotyping of the rice mapping population (BC₁F_2:3) in screenhouse. a Control experiment at 14 DAS, b stress experiment at 14 DAS, c stress experiment at 21 DAS after removing water in the screenhouse, and d stress experiment at 14 DAS in trays-on-table

Fig. 2

Correlation among survivability, seedling height, and germination (control) under screenhouse, tray, and control conditions (NS) for a NSIC Rc238/Kalarata and b NSIC Rc222/Kalarata populations

Fig. 3

a Genetic map of Kalarata/NSIC Rc238 population (left side) and Kalarata/NSIC Rc222 population (right side) showing marker and QTL positions. b Whole-genome scan plots obtained by interval mapping for SUR at 21 DAS in screenhouse conditions for Kalarata/NSIC Rc238 population (left side), and Kalarata/NSIC Rc222 population (right side). Horizontal lines indicate the significant logarithm of odds threshold at 5% and 1% confidence levels (from the bottom to the top) based on 10,000 permutations

Fig. 4

Effect of combinations of qSUR3–1, qSUR6–1, and qSUR7–1 on mean seedling survival under anaerobic conditions at 21 days after seeding. --- refers to lines without the three QTLs, + − - refers to lines with qSUR3–1, − + − refers to lines with qSUR6–1, ++ − refers to lines with qSUR3–1 and qSUR6–1, −− + refers to lines with qSUR7–1, −++ refers to lines with qSUR6–1 and qSUR7–1, and +++ refers to lines with all three QTLs. Letters (“a”, “b” and “c”) above the mean values represent the ranking of each QTL class, where the same letter implies that the mean values are not statistically different

Fig. 5

Whole-genome scan plots by interval mapping for survivability at 21 DAS of the white grain-colored lines of the population Kalarata/NSIC Rc238 (a) and for the population Kalarata/NSIC Rc222 (b) in the screenhouse. Horizontal lines indicate the significant logarithm of odds threshold at 5% and 1% confidence levels (from the bottom to the top) based on 10,000 permutation tests

Fig. 6

Frequency distribution of pericarp color (a) and germination percentage (b) within QTL allele classes across the two populations. + refers to lines with Kalarata allele, − refers to lines with Rc222/Rc238 allele, and H refers to heterozygote for the peak marker of qSUR7–1