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Higher head rice yield HRY , which represents the proportion of intact grains that survive milling, and lower grain chalkiness opacity are key quality traits. We investigated the genetic basis of HRY and chalkiness in diverse resequenced accessions of indica rice with integrated single- and multi-locus genome-wide association studies using 2.
We identified novel haplotypes that underly higher HRY on chromosomes 3, 6, 8, and 11, and that lower grain chalkiness in a fine-mapped region on chromosome 5. Rare and novel haplotypes were found for lowering chalkiness, but missing alleles hindered progress towards enhancing HRY in breeding material.
The novel haplotypes that we identified have potential use in breeding programs aimed at improving these important traits in the rice crop. The annual global production of rice Oryza sativa grown in paddy systems amounts to mt, resulting in mt of polished grains after milling to remove the husk and the bran layers.
To meet the future demands of a growing global population, it is estimated that annual milled rice production needs to increase by additional mt by The lack of sustained adoption of more recently released modern varieties suggests that we not only need to overcome yield stagnation in new varieties Ray et al.
These include a high head rice yield and a low degree of chalkiness, which affects texture Laborte et al. HRY is an important quality trait that can fetch a higher price for farmers due to the net increase in milled whole-grain unbroken yield, especially when this is combined with a lower proportion of chalky grains. Dehulling and milling are important steps in the post-harvest processing of paddy rice, during which the grains are susceptible to fissuring and breakage Buggenhout et al.
Lower intrinsic grain strength leads to higher breakage during grain processing and this is measured as the fracture strength, which is defined as the force that can be tolerated by a grain before it cracks Buggenhout et al. There are many factors that affect HRY, including i post-harvest practices related to the process of grain drying, ii the grain moisture content at harvest, which affects the transition from a more diffusible, rubbery state to a less-diffusible, glassy starch that leads to grain fissuring Cnossen et al.
Although several milling quality traits that exhibit low heritability have been mapped in a subpopulation of japonica species Nelson et al. The dissection of the genetic basis of HRY is important for understanding how kernel susceptibility to breakage can be reduced, and milling quality improved, through marker-assisted breeding in the long, slender grains of indica rice.
Another important grain quality trait is chalkiness, which is generally characterized as an opaque white discoloration in the translucent endosperm caused by the creation of air spaces between irregularly shaped starch granules Butardo and Sreenivasulu, An increased proportion of chalky grains lowers the appearance quality of rice, and is also believed to lower the milling quality by increasing the incidence of grain breakage Del Rosario et al.
Thus, chalkiness has negative impacts on the market value of rice. Grain chalkiness is influenced by genetic and environmental factors Lisle et al. Chalk is a complex and polygenic quantitative trait and several fine-mapped target genes have been shown to influence it, including pyruvate orthophosphate dikinase Kang et al.
Genome-wide association studies GWAS in combination with targeted-gene association studies TGAS have emerged as a two-pronged strategy that can assist in narrowing down the significant trait-specific gene s underlying QTLs and in revealing allelic variants that regulate complex grain-quality traits Butardo et al.
Here, we studied the genetic basis of HRY and chalkiness using combined GWAS single- and multi-locus and gene-set analysis by employing 2. This approach helped to identify key candidate genes that influence the complex genetic architecture of HRY under controlled drying as well as under moisture-stressed conditions. Our findings will assist the future development of high-yielding elite germplasm with superior grain quality and thus contribute to improving the livelihoods of farmers in many developing countries.
A diversity panel of Oryza sativa subsp. The accessions were grown in field plots of Standard crop management procedures were applied.
The samples were then placed at room temperature inside an air-tight plastic ziplock bag for 1 h, after which HRY was determined. Subsamples of grains g, three replicates from the control and moisture stress treatments were dehulled using a Satake dehuller model THUA, Japan with the settings optimized for the different grain shapes. Each sample was then milled using Grainman mill model DT, Miami for 45 s.
The stability value was calculated by dividing the HRY value under stress by the HRY value under controlled condition. The plots were arranged in three replicated randomized blocks, and plants were grown during the dry seasons in and The samples were then evaluated for HRY and other milling quality parameters as described above. Briefly, the lines were grown in field plots during wet and dry seasons according to standard agronomic practice Laborte et al.
The dried samples were evaluated for HRY and chalkiness as described above. After completion of the sequencing process, the raw reads were filtered to remove adaptor sequences and low-quality reads. IRRI conducted in-depth market surveys during — involving rice farmers from Bangladesh, the eastern part of India, Cambodia, and the Philippines Ynion et al.
An interactive tablet application was utilized to assess the priorities of traits for their improvement that farmers would consider before they would replace their most popular current varieties with new ones. The application enabled farmers to design an ideal future variety profile by allocating a fixed investment fund across a portfolio of 11 traits, divided into market-related traits slenderness, aroma, stickiness, and HRY and environment-related traits lodging tolerance, insect resistance, disease resistance, abiotic stress tolerance, reduction of shattering, earliness, and straw digestibility.
A resequenced diversity panel consisting of indica accessions was used for calling of genome-wide SNPs against reference genomes of japonica cv. Genotype files were filtered prior to running the association analysis. To determine the PC, a set of 2. The data from the different seasons were used to check the reproducibility of the results. After running the GWAS on different seasons, we further analysed the results from indica resequenced lines.
The complete parameters used for clumping in plink2 were adapted from Misra et al. Haploview Barrett et al. Haplotype blocks with distinguished phenotype ranges were validated using the SNP-seek database Alexandrov et al.
The translated protein sequences obtained from reference genomes of Nipponbare, MH63, and ZS97 were used for deriving synteny. The longest proteins were selected in cases where splice variants were present. On the basis of these outcomes, colinearity was identified and represented in the form of blocks using Circos Krzywinski et al.
These trends argue for more investment in research focused on unravelling the genetics of HRY. We evaluated a total of breeding lines developed by IRRI between — for HRY and chalkiness by growing them together in dry and wet seasons and subjecting the grain to conditions of controlled drying. While chalkiness was found to be high in varieties released between —, it was substantially lower in modern varieties released between — Fig.
This reduction was due to successful selection made against chalkiness through efficient image-based phenotyping. For varieties released between —, HRY was found to be significantly lower in the dry season that in the wet season Fig. As we did not observe much genetic variation for HRY in existing breeding lines, we examined a diversity panel of resequenced indica lines. The diversity panel showed a high degree of variation for HRY 6. Nevertheless, when the wet and dry season data were combined, the broad-sense heritability for HRY dropped to 0.
PGC ranged from 0. The other milling quality traits showed less variability Supplementary Fig. S1 at JXB online. Thus, strategies employed towards lowering chalkiness alone might not contribute significantly to increase HRY, indicating that it is important to independently examine the underlying genetic variations that contribute to increasing HRY in the pre-breeding pool. Phenotypic variation for milling quality traits in the diversity panel of indica lines and their correlations with grain chalkiness.
The labels at the top indicate the stages during the milling process. Milling fractions include the hull outer seed coat , the removal of which during the dehulling process give rise to brown rice. Blue and red indicate positive and negative correlations, respectively, and the size of the circles and intensity of the colour represent the degree of correlation.
Susceptibility to grain breakage due to induced moisture stress was examined in the lines. These results suggested that variable moisture content in the grain makes long-grain types more susceptible to fracture during milling.
PGC consistently showed a modest positive correlation with grain width under both control and stress conditions Fig. Based on the genotyping data of 2 SNPs obtained from mapping against the japonica reference genome, the GWAS was run for all milling quality traits phenotyped in the indica lines under controlled drying and moisture stressed conditions from dry season.
Using the genotyping data from the two indica reference genomes, we confirmed that the peaks detected in chromosomes 6 and 8 associated with HRY. The loci on chromosomes 6, 8, and 11 only using the Nipponbare reference were further confirmed by multi-locus GWAS and are indicated by red arrows. Scaled log 10 P values are shown and the red bars indicate a relative negative effect.
Significantly associated genomic regions for HRY identified in our study highlighted as red blocks and in previous studies pink block along with the stability-associated genomic region grey blocks are indicated; green stripes indicate conserved regions, while white indicates collinearity breaks in the region. Chromosome 6 The fine-mapped genomic region at An additional fine-mapped 9. In addition to HRY, the genomic regions that contributed to other milling quality traits under controlled drying conditions were related to PMR and WMR, which were mapped on chromosome 8 6.
Gene-set analysis using GWAS of candidates identified within the hotspot genomic regions on chromosomes 3, 6, 8, and 11 associated with head rice yield. Single-locus GWAS and gene-set analysis were performed to identify genomic regions regulating the stability HRY ratio of moisture stress and control along with covariate of HRY values obtained from controlled drying conditions.
The HRY stable regions were mapped to a The significant peak was further confirmed by multi-locus GWAS using the two indica reference genomes Fig. The hotspot genomic region represented by the second LD-block was found to be negatively regulating the stability trait Fig.
Furthermore, the haplotypes identified in the key candidates for influencing HRY on chromosomes 6, 8, and 11 showed consistent behavior across dry and wet seasons Supplementary Fig. Gene-set analysis using GWAS of identified candidates within the hotspot genomic region on chromosomes 8 that regulate stability under moisture stress conditions. Under stress conditions, GWAS identified a key region on chromosome 1 Another association peak was identified on an We assessed the level of structural variation that existed in the target regions on chromosomes 3, 6, 8, and 11 between japonica Nipponbare and indica ZS97 reference genomes, and identified collinearity and break-points in the respective genomes Fig.
The chromosome 8 hotspot region was located in the conserved regions. Notably, we detected several break-points between ZS97 and Nipponbare, especially within the target hotspot regions for HRY traits mapped on chromosomes 3, 6, and 11 Supplementary Fig.
This suggested the existence of structural variations in the genetic regions that regulate HRY, which reinforced the importance of using subspecies-based reference genome s for genotype calling to conduct targeted associations.
S7 , red arrows. Gene-set analysis identified a highly significant Z -score for chalk5. TGAS of chalk5. This region chalk5. When we mapped the chalkiness hotspot region that showed colinearity on chromosome 5, we observed several break-points between high chalkiness ZS97 and low chalkiness Nipponbare reference genomes within the target hotspot region for PGC on chromosome 5 Fig. This indicated the role of existing structural variations underlying the hotspot region in regulating grain chalkiness.
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All alleles are reported in the Forward orientation. HGVS names are in the Aliases tab. Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors. For more information see Help documentation. The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted.
Dissecting the genome-wide genetic variants of milling and appearance quality traits in rice