
Rice grain quality is a complex trait that involves grain physical appearance, milling quality, eating and cooking quality, and nutritional quality. Among them, nutritional quality as well as eating and cooking qualities (ECQs) play significant indices to consumer’s preference and market-place (Yang
Association between starch properties and natural variation in starch synthesis–related genes had already been confirmed in various studies. The
Asian cultivated rice is widely grown and is divided into two major sub-species,
Protein disulfide isomerase (PDI) is a chaperone protein that plays a significant function in protein folding in endoplasmic reticulum (ER) (Yagi-Utsumi
In this study, we investigated the association of
In our previous study, we established a RIL population by crossing two closely related
Here, our study mainly focused on QTL found on chro-mosome 11. All genes covering the
Total genomic DNA was extracted from fresh leaves of each cultivar using the cetyltrimethylammonium bromide (CTAB) method as described by Murray and Thompson (1980). To determine whether plants are possessing the
To detect the
To detect the
The amylose content of F3 seeds was measured using the Megazyme assay kit (Megazyme Ltd., Wicklow, Ireland), following the manufacturer’s instructions and was analyzed in Plant Breeding and Genetics laboratory, Chungnam National University. The amylose content of Korean
All analyses i.e. one-way analysis of variance and correlation analysis were carried out using MINITAB 16.2.4 software.
In our previous work, we conducted QTL mapping and identified QTLs associated with AC in a recombinant inbred line (RIL) population derived from two
Whole genome sequencing of parental lines, Dodamssal and Hwayeong, was determined with reference to the Nipponbare reference genome. Sequencing results led to the identification of various amylose-linked SNPs/InDels in
By excluding lines with a
Table 1 . Characteristic of the
SNP ID | Chr | Physical position (bp) | Year | Genotypex) | |
---|---|---|---|---|---|
DD | HH | ||||
G/A | 11 | -4973180 | 2017 | 16.1 ± 2.60 | 14.3 ± 2.09* |
2018 | 16.2 ± 1.23 | 15.2 ± 1.45* |
x)DD: Dodamssal homozygous, HH: Hwayeong homozygous. * indicates significant difference at
Amylose content is the key factor that controls ECQs in rice while protein content plays a significant role in rice nutritional quality. In our present study, we determined the AC in 29 F2 plants and AC, PC, and days to heading (DTH) in 160 Korean
Previous studies have reported a correlation between AC and heading date and between AC and PC. Rice quality is affected by the mean temperature during the grain filling stage, which is determined by the heading date. High temperature (30℃) occurring at the early-filling stage hampered starch synthesis and accumulation that resulted in the formation of chalky seeds with low AC, while lower temperatures (22℃) occurring at the late-filling stage allowed starch synthesis and accumulation to revert to normal levels. In RILs possessing the
Table 2 . Correlation analysis between amylose content (AC) and days to heading (DTH) of RILs in a two-year field experiment.
Trait | 2017 AC | 2018 AC | 2017 DTH |
---|---|---|---|
2018 AC | 0.376* | ||
2017 DTH | 0.432* | 0.411* | |
2018 DTH | 0.404* | 0.221 | 0.769*** |
* and *** indicate significant differences at
Table 3 . Correlation analysis between amylose content (AC), protein content (PC), and days to heading (DTH) of 160 Korean
Traits | AC | PC |
---|---|---|
PC | ‒0.061 | |
DTH | 0.552*** | ‒0.198* |
* and *** indicate significant differences at
Functional markers (FMs) were developed using the SNPs identified between Dodamssal and Hwayeong. Three gene-based molecular markers, namely one CAPs (Fig. 4A) and two InDel markers (Figs. 4B and 4C) were designed. The CAPs marker targeted the position of -4973180 (G/A SNP) of
To detect the ATTCG/G at intron 1 of
Prior to analysis, all plants/cultivars possessing the
Table 4 . Comparison of amylose content between two genotypes classified based on SNP/InDel at
Group | No. of F2 plants | Position (bp) and SNP (InDel) | % AC | |
---|---|---|---|---|
-4973180 | -4974161 | |||
I | 2 | G | ATTCG | 13.2 ± 0.07 |
II | 10 | A | G | 14.2 ± 0.70 |
0.02* | 0.03* | 0.02* |
Percentage of amylose content (%AC) was presented as mean ± standard deviation.
* indicates significant difference at
Out of 164, a total of 161
At position -4973180, Korean
Table 5 . Comparison of amylose and protein content among groups classified based on each SNP and their combination of InDel and SNP.
Group | No. of Korean | -4973180 | -4974161 | % ACx) | % PCy) | ||
---|---|---|---|---|---|---|---|
Nucleotide | G/A | ATTCG/G | |||||
Group I | 100 | G | ATTCG | 18.4 ± 0.9a | 6.3 ± 0.5a | ||
Group II | 35 | G | G | 18.8 ± 1.1a | 6.5 ± 0.5a | ||
Group III | 25 | A | G | 17.5 ± 0.8b | 6.4 ± 0.4a | ||
% AC | 0.000*** | 0.472ns | 0.000*** | ||||
% PC | 0.699ns | 0.037* | 0.074ns |
Percentage of amylose content (%AC) and protein content (%) was presented as mean ± standard deviation. * and *** indicate significant differences at
Rice is a widely grown crop and extensive varietal differences in eating quality characteristics had been discovered in worldwide rice germplasm accessions including
In this study, with the aim of identifying other genes involved in starch biosynthesis that can affect the amylose content in
To date, identification and characterization of new molecular markers associated with amylose content regulation has been wide-ranging. There have been several reported molecular markers that can distinguish rice cultivars based on their amylose content. Bligh
The newly developed markers in our present study could benefit breeding programs by introducing the
In rice, PC is one of the key factors affecting the eating and cooking qualities. Previous study reported that in common rice grains, there is highly significant negative correlation between amylose content and protein content (Li
This study investigated the association of
This work was carried out with the support of “Coo-perative Research Program for Agriculture Science and Technology Development (Project No. PJ015757)” Rural Development Administration, Republic of Korea.
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