Grain Fe and Zn contents linked SSR markers based genetic diversity in rice

Rice is critical for sustainable food and nutritional security; however, nominal micronutrient quantities in grains aggravate malnutrition in rice-eating poor populations. In this study, we evaluated genetic diversity in grain iron (Fe) and zinc (Zn) contents using trait-linked simple sequence repeat (SSR) markers in the representative subset of a large collection of local and exotic rice germplasm. Results demonstrated that aromatic fine grain accessions contained relatively higher Fe and Zn contents in brown rice (BR) than coarse grain accessions and a strong positive correlation between both mineral elements. Genotyping with 24 trait-linked SSR markers identified 21 polymorphic markers, among which 17 demonstrated higher gene diversity and polymorphism information content (PIC) values, strongly indicating that markers used in current research were moderate to highly informative for evaluating the genetic diversity. Population structure, principal coordinate and phylogenetic analyses classified studied rice accessions into two fine grain specific and one fine and coarse grain admixture subpopulations. Single marker analysis recognized four ZnBR and single FeBR significant marker-trait associations (MTAs) contributing 15.41–39.72% in total observed phenotypic variance. Furthermore, high grain Fe and Zn contents linked marker alleles from significant MTAs were also identified. Collectively, these results indicate a wide genetic diversity exist in grain Fe and Zn contents of studied rice accessions and reveal perspective for marker-assisted biofortification breeding.

quantities in grains aggravate malnutrition in rice-eating poor populations. Here, we assessed 11 genetic diversity in grain iron (Fe) and zinc (Zn) contents using trait-linked simple sequence 12 repeat (SSR) markers in fine and coarse grain rice accessions of different geographical origin. Rice is one of the most consumed food crops globally, especially in developing countries [1].

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The world population is increasing at an exponential rate; however, current annual genetic gain 31 in rice production is insufficient to meet future food requirements [2], demanding continuous 32 efforts to breed high yielding and more nutritious rice cultivars. Thus, there is an urgent need 33 to boost global rice production, along with nutritional quality, for sustainable food and   Pakistan, China and India were used in this study (S1 Table). The seed of these accessions was

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To determine Fe and Zn contents, brown rice samples of 56 indica accessions (S1 Table) were 124 processed through a wet-chemical digestion method and the extract was fed to atomic 125 absorption spectrophotometer. Significant genetic variability existed among studied accessions 126 for grain Fe and Zn contents (Fig 1A). Fe contents varied from 5.45 ppm (PK 10967) to 52.30  (Fig 1B). Nearly, 18% and 23% of the total 131 accessions contained > 30 ppm Fe and Zn densities respectively, and the majority of these had 132 fine grains. Furthermore, significant positive correlation (r = 0.757, p < 0.001) was present 133 between grain Fe and Zn contents (Fig 1C). These results indicate availability of significant      (Fig 3) and UPGMA phylogenetic (Fig 4) analyses also supported population structure 173 results. The SP1 and SP2 harboured 20 and 10 fine grain accessions. Likewise, SP3 also 174 harboured 25 fine and coarse grain accessions. Unexpectedly, one Chinese-originated coarse 175 grain genotype (UHL17078; serial # 51) also clustered with fine grain genotypes of SP2 ( Fig   176   3 and 4), which could be due to more similar DNA banding patterns of this genotype with fine 177 grain accessions than with coarse grain genotypes. In UPGMA phylogenetic tree, more than 178 72% (16) of the total (22) high grain Fe and Zn rice accessions (containing > 30 ppm) were 179 clustered into SP1 and SP2, whereas less than 28% (6) grouped into SP3 (Fig 4). Collectively, 180 these results strongly indicate that fine grain rice accessions contain relatively higher 181 micronutrient contents as compared with coarse grain accessions.      brown rice (Fig 1A), which is in accordance with recent reports [13,36]. The Fe and Zn 231 contents in unpolished grains of fine/aromatic rice accessions were relatively higher than 232 coarse grain accessions (Fig 1B). Gregorio  reported higher Fe and Zn contents in aromatic rice cultivars than non-aromatic cultivars.

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Significant positive correlation was present between Fe and Zn contents (Fig 1C).  (Fig 3) and phylogenetic (Fig 4)  and coarse grain accessions. These results suggest that trait linked markers used in this study 261 might be also good for genetic differentiation between fine and coarse grain genotypes.

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Moreover, the majority of the high grain Fe and Zn accessions (containing > 30 ppm) were 263 grouped into SP1 and SP2 (Fig 4) contents than their all other respective alleles (Fig 5). Similarly, significantly higher grain Fe 287 contents were observed in 200 bp allele containing rice accessions, which were genotyped with 288 RM 501. Our results suggest that these alleles could be used for screening of high grain Fe and 289 Zn containing rice germplasm and marker-assisted development of biofortified rice cultivars.

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To the best of our knowledge, this is the first report on comparison of SSR marker alleles with 291 grain micronutrient contents in rice. Therefore, these results should be validated using large 292 and diverse population sets before practical application in marker-assisted biofortification 293 breeding in rice. The authors declare that they have no competing interests. Click here to download Figure Fig 1.tif