Junliang Zhao^1,2†, Wu Yang^1,2†,
Shaohong Zhang^1,2, Tifeng Yang^1,2, Qin Liu^1,2,
Jingfang Dong^1,2, Hua Fu^1,2,Xingxue Mao^1,2 and
Bin Liu^1,2*

Rice

Background：Cadmium (Cd) accumulation in rice followed
by transfer to the food chain causes severe health problems in humans. Breeding
of low Cd accumulation varieties is one of the most economical ways to solve
the problem. However, information on the identity of rice germplasm with low Cd
accumulation is limited, particularly in indica, and the genetic basis of Cd
accumulation in rice is not well understood. 

Results：Screening of 312 diverse rice accessions
revealed that the grain Cd concentrations of these rice accessions ranged from
0.12 to 1.23 mg/kg, with 24 accessions less than 0.20 mg/kg. Three of the 24
accessions belong to indica. Japonica accumulated significantly less Cd than
indica (p < 0.001), while tropical japonica accumulated significantly less
Cd than temperate japonica (p < 0.01). GWAS in all accessions identified 14
QTLs for Cd accumulation, with 7 identified in indica and 7 identified in
japonica subpopulations. No common QTL was identified between indica and
japonica. The previously identified genes (OsHMA3, OsNRAMP1, and OsNRAMP5) from
japonica were colocalized with QTLs identified in japonica instead of indica.
Expression analysis of OsNRAMP2, the candidate gene of the novel QTL (qCd3–2)
identified in the present study, demonstrated that OsNRAMP2 was mainly induced
in the shoots of high Cd accumulation accessions after Cd treatment. Four amino
acid differences were found in the open reading frame of OsNRAMP2 between high
and low Cd accumulation accessions. The allele from low Cd accumulation
accessions significantly increased the Cd sensitivity and accumulation in
yeast. Subcellular localization analysis demonstrated OsNRAMP2 expressed in the
tonoplast of rice protoplast. 

Conclusion：The results suggest that grain Cd
concentrations are significantly different among subgroups, with Cd
concentrations decreasing from indica to temperate japonica to tropical
japonica. However, considerable variations exist within subgroups. The fact
that no common QTL was identified between indica and japonica implies that
there is a different genetic basis for determining Cd accumulation between
indica and japonica, or that some QTLs for Cd accumulation in rice are
subspecies-specific. Through further integrated analysis, it is speculated that
OsNRAMP2 could be a novel functional gene associated with Cd accumulation in
rice. 

Keywords：Rice (Oryza sativa L.)  Cadmium accumulation   Quantitative trait locus (QTL)   Genome-wide association study (GWAS)

附件：Genome-wide association study and candidate gene analysis of rice cadmium accumulation in grain in a diverse rice collection