Research Article: Genomic prediction offers the most effective marker assisted breeding approach for ability to prevent arsenic accumulation in rice grains

Date Published: June 13, 2019

Publisher: Public Library of Science

Author(s): Julien Frouin, Axel Labeyrie, Arnaud Boisnard, Gian Attilio Sacchi, Nourollah Ahmadi, Jauhar Ali.


The high concentration of arsenic (As) in rice grains, in a large proportion of the rice growing areas, is a critical issue. This study explores the feasibility of conventional (QTL-based) marker-assisted selection and genomic selection to improve the ability of rice to prevent As uptake and accumulation in the edible grains. A japonica diversity panel (RP) of 228 accessions phenotyped for As concentration in the flag leaf (FL-As) and in the dehulled grain (CG-As), and genotyped at 22,370 SNP loci, was used to map QTLs by association analysis (GWAS) and to train genomic prediction models. Similar phenotypic and genotypic data from 95 advanced breeding lines (VP) with japonica genetic backgrounds, was used to validate related QTLs mapped in the RP through GWAS and to evaluate the predictive ability of across populations (RP-VP) genomic estimate of breeding value (GEBV) for As exclusion. Several QTLs for FL-As and CG-As with a low-medium individual effect were detected in the RP, of which some colocalized with known QTLs and candidate genes. However, less than 10% of those QTLs could be validated in the VP without loosening colocalization parameters. Conversely, the average predictive ability of across populations GEBV was rather high, 0.43 for FL-As and 0.48 for CG-As, ensuring genetic gains per time unit close to phenotypic selection. The implications of the limited robustness of the GWAS results and the rather high predictive ability of genomic prediction are discussed for breeding rice for significantly low arsenic uptake and accumulation in the edible grains.

Partial Text

Presence of high concentration of arsenic (As) in the paddy fields or in the irrigation water (>20 mg Kg-1 and 0.10 mg Kg-1, respectively) has been reported in more than 70 countries in Asia, America and Europe [1–3]. The problem, often of geological origin, affects several hundred million peoples living in the area, especially in Asia [1, 3, 4] as it translates into rice grain. Local and regional surveys have revealed tight correlation between As concentration in the cultivated soil, or in the irrigation water, and in the rice plant [2, 5]. As accumulation in the rice plant is the highest in the roots, followed by the straw, the whole (cargo) grain and the polished (white) grain [2, 5, 6]. Presence of As in the paddy field also affects crop growth and development and, consequently, crop yield [6].

The aim of this work was to explore (i) the phenotypic diversity of the rice japonica subspecies, adapted to cultivation in Mediterranean Europe, to restrict As accumulation in the edible grains, and (ii) the potential of the two major options of marker-assisted selection for the improvement of the trait, i.e. QTL-based selection and genomic estimate of breeding value (GEBV)-based selection.