Cadmium (Cd) accumulation in rice is a serious threat to food safety and human health. Breeding rice varieties with low Cd accumulation is one of the most effective approaches to reducing health risks from Cd-polluted rice. However, the genetic basis of Cd accumulation in grains, especially in indica rice varieties, has not been fully elucidated. The evaluation of Cd-accumulation capacity was conducted among 338 diverse rice accessions grown in Cd-contaminated soils with different Cd contents. Thirteen rice lines with relatively low Cd accumulation, including six indica rice lines, were identified. Then, 35 QTLs significantly associated with Cd accumulation were identified through sequencing-based SNP discovery and a genome-wide association study (GWAS) in the two experimental years, and only qCd8-1 was detected in both years. Among of them, nine QTLs were co-localized with identified genes or QTLs. A novel QTL, qCd1-3, with the lowest P value was selected for further LD decay analysis and candidate gene prediction. We found differential expression of OsABCB24 between high-Cd-accumulative and low-Cd-accumulative accessions, suggesting it may be a candidate gene for qCd1-3 associated with low Cd accumulation. These results may be helpful for further exploiting novel functional genes related to Cd accumulation and developing rice variety with low Cd accumulation through marker-assisted breeding.

Sheath blight ( SB ) is one of the most destructive rice diseases that affect the yield and quality of rice. J asmonate and E thylene R esponse F actor 1 , designated JERF 1 , can be induced by ethylene, methyl jasmonate ( M e JA ), abscisic acid (ABA) and salt stress. Previous research demonstrated that over‐expression of JERF 1 enhanced drought tolerance by regulating the expression of stress‐related genes in rice. The present study reports that JERF 1 could improve SB resistance of transgenic rice. At the molecular and physiological levels, JERF 1 could up‐regulate the expression of signalling and defence‐related genes and increase the activities of lipoxygenase ( LOX ) and phenylalanine ammonia lyase ( PAL ). Analysis of cis ‐elements showed that there were several DRE / CRT (dehydration‐responsive element/ C ‐repeat) and/or GCC boxes in the promoters of these candidate genes, indicating that JERF 1 might regulate the expression of defence‐related genes via interaction with these cis ‐elements. These results suggest that JERF 1 might improve SB resistance by modulating the expression of defence‐related genes. This may prove to be a useful strategy for genetic engineering to improve SB resistance using transcription factor genes in rice.

The accumulation of arsenic (As) in rice poses a significant threat to food safety and human health. Breeding rice varieties with low As accumulation is an effective strategy for mitigating the health risks associated with arsenic-contaminated rice. However, the genetic mechanisms underlying As accumulation in rice grains remain incompletely understood. We evaluated the As accumulation capacity of 313 diverse rice accessions grown in As-contaminated soils with varying As concentrations. Six rice lines with low As accumulation were identified. Additionally, a genome-wide association studies (GWAS) analysis identified 5 QTLs significantly associated with As accumulation, with qAs4 being detected in both of the experimental years. Expression analysis demonstrated that the expression of LOC_Os04g50680, which encodes an MYB transcription factor, was up-regulated in the low-As-accumulation accessions compared to the high-As-accumulation accessions after As treatment. Therefore, LOC_Os04g50680 was selected as a candidate gene for qAs4. These findings provide insights for exploiting new functional genes associated with As accumulation and facilitating the development of low-As-accumulation rice varieties through marker-assisted breeding.

Grain shape is usually characterized by grain length (GL), grain width (GW), grain thickness (GT) and length to width ratio (LWR), and controlled by quantitative trait locus (QTL). In this paper, QTL analysis was performed using an F2 population and an F8 recombinant inbred line (RIL) population from a cross Xiang743/Katy. A total of 38 QTLs for grain shape were detected and eight of them were repeatedly identified in both populations. Seven for GL, five for GW, five for GT, and eight for LWR were detected in F2 population, explaining totally phenotypic variance of 94.51%, 61.52%, 54.33% and 91.84%, respectively. Five for GL, three for GW, and five for LWR were detected in RILpopulation, explaining totally phenotypic variance of 39.83%, 37.52% and 36.71%, respectively. Many QTLs were located in similar intervals, contributing to complicated trait correlation. A few QTLs were mapped in intervals coincided with previously cloned genes associated with grain size. Two residual heterozygous lines (RHLs) were selected out on the basis of newly identified loci, populations derived from RHLs were constructed for fine mapping QTLs associated with grain shape.