Map-based cloning of a new total loss-of-function allele of OsHMA3 causes high cadmium accumulation in rice grain

Sui, Fuqing; Zhao, Di-Kun; Zhu, Haitao; Gong, Yongfu; Tang, Zhong; Huang, Xin‐Yuan; Zhang, Guiquan; Zhao, Fang‐Jie

doi:10.1093/jxb/erz093

Cited by 60 publications

(46 citation statements)

References 46 publications

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“…In the past two decades, we have constructed a SSSL library by the using of HJX74 as the recipient and 43 accessions from 7 species, including 5 wild Oryza species of AA genome as donors (Zhang et al 2004;Xi et al 2006;Zhang 2019). The SSSLs have been used to map QTLs (Zhang et al 2012;Yang et al 2016;Zhou et al 2017b), to clone genes (Wang et al 2012;Sui et al 2019), and to analyze allelic variation (Teng et al 2012;Cai et al 2013). Based on the SSSL library, we have developed a platform of breeding by design for cytoplasmic male sterility (CMS) lines and restorer lines, and a series of CMS lines and restorer lines were developed (Dai et al 2015(Dai et al , 2016Luan et al 2019).…”

Section: Discussionmentioning

confidence: 99%

Substitution mapping of the major quantitative trait loci controlling stigma exsertion rate from Oryza glumaepatula

Tan

Zou

Zheng

et al. 2020

Preprint

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Background: Stigma exsertion rate (SER) is a key determinant for the outcrossing ability of male sterility lines (MSLs) in hybrid rice seed production. In the process of domestication, the outcrossing ability of cultivated rice varieties decreased, while that of wild Oryza species kept strong. Here, we detected the quantitative trait loci (QTLs) controlling SER using a set of single-segment substitution lines (SSSLs) derived from O. glumaepatula , a wild Oryza species. Results: Seven QTLs for SER were located on 5 chromosomes. qSER-1a and qSER-1b were located on chromosome 1. qSER-3a and qSER-3b were mapped on chromosome 3, and qSER-3b was further located at an estimated interval of 898.8kb by secondary substitution mapping. qSER-5 , qSER-9 and qSER-10 were identified on chromosomes 5, 9 and 10, respectively, and qSER-9 was delimited to an estimated region of 551.9kb by secondary substitution mapping. The additive effects of the 7 QTLs ranged from 10.6% to 14.8%, which were higher than those of most loci for SER reported previously. Conclusions: qSER-1a and qSER-1b are novel loci for SER on chromosome 1. All of the 7 QTLs have major effects on SER. The major QTLs of SER will help to develop MSLs with strong outcrossing ability.

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Section: Discussionmentioning

confidence: 99%

Substitution mapping of the major quantitative trait loci controlling stigma exsertion rate from Oryza glumaepatula

Tan

Zou

Zheng

et al. 2020

Preprint

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“…To date, genes underlying several QTLs for Cd accumulation in rice have been cloned [40][41][42] . OsHMA3, encoding a tonoplast Cd transporter, is a key gene controlling Cd translocation from roots to shoots and grain in rice; weak alleles of OsHMA3 are associated with high accumulation of Cd in rice grain [40,[43][44][45] . Strong alleles of OsHMA3 can be used to breed low Cd rice cultivars.…”

Section: Breeding or Engineering Crop Cultivars With Low Metal(loid) mentioning

confidence: 99%

Strategies to manage the risk of heavy metal(loid) contamination in agricultural soils

Zhao¹

2020

Front. Agr. Sci. Eng.

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Soil contamination with heavy metal(loid)s threatens soil ecological functions, water quality and food safety; the latter is the focus of this review. Cadmium (Cd) and arsenic (As) are the toxic elements of most concern for food safety because they are relatively easily taken up by food crops. Rice is a major contributor of both Cd and As intakes to the Chinese population. Contamination and soil acidification are the main causes of high Cd levels in rice grains produced in some areas of southern China. The risk of Cd and As accumulation in food crops can be mitigated through agronomic practices and crop breeding. Liming is effective and economical at reducing Cd uptake by rice in acid soils. Paddy water management can produce opposite effects on Cd and As accumulation. Many genes controlling Cd and As uptake and translocation have been characterized, paving the way to breeding low accumulating crop cultivars through marker-assisted molecular breeding or genetic engineering. It is important to protect agricultural soils from future contamination. Long-term monitoring of anthropogenic additions and accumulation of heavy metal(loid)s in agricultural soils should be undertaken. Mass-balance models should be constructed to evaluate future trends of metal(loid)s in agricultural soils at a regional scale.

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“…Liu et al 16 identified seven QTLs and validated qCd2 associated with grain Cd content using a recombinant inbred line (RIL) population. Another major QTL (qCd7) was repeatedly detected using different genetic populations and finally cloned [17][18][19][20] . The candidate gene of qCd7, OsHMA3, encodes a tonoplast-localized P 1B -type ATPase.…”

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QTL mapping and candidate gene analysis of cadmium accumulation in polished rice by genome-wide association study

Pan

Liu

et al. 2020

Sci Rep

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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. Rice (Oryza sativa L.) is one of the world's staple food crops. Due to rapid industrialization and urbanization in recent years, heavy metal contamination in arable soils has become an increasingly severe problem in China. Among the heavy metals, cadmium (Cd) is the most serious contaminant. Reportedly, average Cd concentrations in paddy fields of China reached 0.23 mg/kg, and the highest concentration of 0.73 mg/kg was recorded from Hunan province 1. Recently, Cd-polluted rice from Hunan, the largest rice-producing province in China, has become a particular concern in food safety. It has been reported that rice tends to accumulate more Cd than other cereals 2. Moreover, the acidification of paddy soil caused by frequent applications of nitrogen fertilizer increases Cd solubility and results in more Cd absorption by rice plants 3. In rice, Cd inhibits growth and development by causing misfolding of functional proteins and interfering the homeostasis of other essential metal ions 4. For people, excessive accumulation of Cd may result in diseases such as cancer, anemia, heart failure, hypertension, as well as other chronic disorders 5,6. A range of measures have been adopted to reduce Cd bioaccumulation, including soil remediation, Cd immobilization and transgenic techniques. The most promising strategy is to screen and breed rice varieties with low Cd accumulation, especially crops grown on slightly to moderately Cd-contaminated soils 2. Genetic variation naturally occurs among rice varieties in their abilities to accumulate Cd. Thus, extensive screening has been carried out to identify rice genetic resources with low Cd acc...

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Map-based cloning of a new total loss-of-function allele of OsHMA3 causes high cadmium accumulation in rice grain

Cited by 60 publications

References 46 publications

Substitution mapping of the major quantitative trait loci controlling stigma exsertion rate from Oryza glumaepatula

Substitution mapping of the major quantitative trait loci controlling stigma exsertion rate from Oryza glumaepatula

Strategies to manage the risk of heavy metal(loid) contamination in agricultural soils

QTL mapping and candidate gene analysis of cadmium accumulation in polished rice by genome-wide association study

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