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

ABSTRACT: 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.

SUBMITTER: Frouin J

PROVIDER: S-EPMC6563978 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The gram pod borer Helicoverpa armigera is a major constraint to chickpea (Cicer arietinum L.) production worldwide, reducing crop yield by up to 90%. The constraint is difficult to overcome as chickpea germplasm including wild species either lacks pod borer resistance or if possessing resistance is cross-incompatible. This study describes conversion of elite but pod borer-susceptible commercial chickpea cultivars into resistant cultivars through introgression of cry1Ac using marker-assisted backcross breeding. The chickpea cultivars (PBG7 and L552) were crossed with pod borer-resistant transgenic lines (BS 100B and BS 100E) carrying cry1Ac that led to the development of BC1F1, BC1F2, BC1F3, BC2F1, BC2F2, and BC2F3 populations from three cross combinations. The foreground selection revealed that 35.38% BC1F1 and 8.4% BC1F2 plants obtained from Cross A (PBG7 × BS 100B), 50% BC1F1 and 76.5% BC1F2 plants from Cross B (L552 × BS 100E), and 12.05% BC2F2 and 82.81% (average) BC2F3 plants derived from Cross C (PBG7 × BS 100E) carried the cry1Ac gene. The bioassay of backcross populations for toxicity to H. armigera displayed up to 100% larval mortality. BC1F1 and BC1F2 populations derived from Cross B and BC2F3 population from Cross C segregated in the Mendelian ratio for cry1Ac confirmed inheritance of a single copy of transgene, whereas BC1F1 and BC1F2 populations obtained from Cross A and BC2F2 population from Cross C exhibited distorted segregation ratios. BC1F1 plants of Cross A and Cross B accumulated Cry1Ac protein ranging from 11.03 to 11.71 µgg-1 in leaf tissue. Cry1Ac-positive BC2F2 plants from Cross C demonstrated high recurrent parent genome recovery (91.3%) through background selection using SSR markers and phenome recovery of 90.94%, amongst these 30% plants, were homozygous for transgene. The performance of BC2F3 progenies derived from homozygous plants was similar to that of the recurrent parent for main agronomic traits, such as number of pods and seed yield per plant. These progenies are a valuable source for H. armigera resistance in chickpea breeding programs.

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

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