Genome-wide association analysis reveals new targets for carotenoid biofortification in maize.
Genome-wide association analysis reveals new targets for carotenoid biofortification in maize.
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DOI：
10.1007/s00122-015-2475-3
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发表时间：
2015-05
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影响因子：
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通讯作者：
Babu R
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作者：
Suwarno WB;Pixley KV;Palacios-Rojas N;Kaeppler SM;Babu R
CIMMYT 关联小组中的全基因组关联分析揭示了羟化酶和 CCD1 等重要基因中/附近新的有利的天然基因组变异，这些基因具有玉米中类胡萝卜素生物强化的潜力。 全基因组关联研究（GWAS）已被广泛用于识别控制植物重要农艺和营养性状的基因的等位基因变异。维生素原 A (proVA) 增强番茄红素 epsilon 环化酶 (LCYE) 和 β-胡萝卜素羟化酶 1 (CRTRB1) 等位基因，先前通过基于候选基因的 GWAS 鉴定出，目前用于 CIMMYT 的玉米育种计划。本研究的目的是使用具有约 476,000 个 SNP 标记的高密度全基因组平台，为 CIMMYT 的 380 个自交玉米系的类胡萝卜素关联作图小组确定控制谷物中类胡萝卜素浓度变异的基因或基因组区域。通过使用主成分和亲属关系矩阵与混合模型进行调整，将人口结构影响降至最低。全基因组连锁不平衡 (LD) 分析表明 LD 衰减（3.9 kb；r 2 = 0.1）比通常报道的温带种质更快，因此我们的主要热带多样性面板有可能实现更高的作图分辨率。各种类胡萝卜素的 GWAS 鉴定了 CRTRB1、LCYE 和其他控制上游途径中关键速率步骤的关键基因或基因组区域，例如 DXS1、GGPS1 和 GGPS2（已知它们在前体类异戊二烯的积累中发挥重要作用）以及下游基因 HYD5、CCD1 和 ZEP1（参与羟基化和类胡萝卜素降解）。所有这些区域或附近的 SNP 均已确定，并且可能是玉米类胡萝卜素生物强化育种工作的有用目标区域；例如，2 号染色体上的基因组区域独立于 CRRTB1 解释了 β-胡萝卜素约 16% 的表型变异，并且在先前观察到 proVA 降解率较低的品系中发现了导致 β-隐黄质降解减少的 CCD1 变体。本文的在线版本 (doi:10.1007/s00122-015-2475-3) 包含补充材料，可供授权用户使用。
Genome-wide association analysis in CIMMYT’s association panel revealed new favorable native genomic variations in/nearby important genes such as hydroxylases and CCD1 that have potential for carotenoid biofortification in maize. Genome-wide association studies (GWAS) have been used extensively to identify allelic variation for genes controlling important agronomic and nutritional traits in plants. Provitamin A (proVA) enhancing alleles of lycopene epsilon cyclase (LCYE) and β-carotene hydroxylase 1 (CRTRB1), previously identified through candidate-gene based GWAS, are currently used in CIMMYT’s maize breeding program. The objective of this study was to identify genes or genomic regions controlling variation for carotenoid concentrations in grain for CIMMYT’s carotenoid association mapping panel of 380 inbred maize lines, using high-density genome-wide platforms with ~476,000 SNP markers. Population structure effects were minimized by adjustments using principal components and kinship matrix with mixed models. Genome-wide linkage disequilibrium (LD) analysis indicated faster LD decay (3.9 kb; r 2 = 0.1) than commonly reported for temperate germplasm, and therefore the possibility of achieving higher mapping resolution with our mostly tropical diversity panel. GWAS for various carotenoids identified CRTRB1, LCYE and other key genes or genomic regions that govern rate-critical steps in the upstream pathway, such as DXS1, GGPS1, and GGPS2 that are known to play important roles in the accumulation of precursor isoprenoids as well as downstream genes HYD5, CCD1, and ZEP1, which are involved in hydroxylation and carotenoid degradation. SNPs at or near all of these regions were identified and may be useful target regions for carotenoid biofortification breeding efforts in maize; for example a genomic region on chromosome 2 explained ~16 % of the phenotypic variance for β-carotene independently of CRTRB1, and a variant of CCD1 that resulted in reduced β-cryptoxanthin degradation was found in lines that have previously been observed to have low proVA degradation rates. The online version of this article (doi:10.1007/s00122-015-2475-3) contains supplementary material, which is available to authorized users.