Key message

Genome wide association studies allowed prediction of 17 candidate genes for association with nitrogen use efficiency. Novel information obtained may provide better understanding of genomic controls underlying germplasm variations for this trait in Indian mustard.

Abstract

Nitrogen use efficiency (NUE) of Indian mustard (Brassica juncea (L.) Czern & Coss.) is low and most breeding efforts to combine NUE with crop performance have not succeeded. Underlying genetics also remain unexplored. We tested 92 SNP-genotyped inbred lines for yield component traits, N uptake efficiency (NUPEFF), nitrogen utilization efficiency (NUTEFF), nitrogen harvest index (NHI) and NUE for two years at two nitrogen doses (N_o without added N and N₁₀₀ added @100 kg/ha). Genotypes IC-2489-88, M-633, MCP-632, HUJM 1080, GR-325 and DJ-65 recorded high NUE at low N. These also showed improved crop performance under high N. One determinate mustard genotype DJ-113 DT-3 revealed maximum NUTEFF. Genome wide association studies (GWAS) facilitated recognition of 17 quantitative trait loci (QTLs). Environment specificity was high. B-genome chromosomes (B02, B03, B05, B07 and B08) harbored many useful loci. We also used regional association mapping (RAM) to supplement results from GWAS. Annotation of the genomic regions around peak SNPs helped to predict several gene candidates for root architecture, N uptake, assimilation and remobilization. CAT9 (At1g05940) was consistently envisaged for both NUE and NUPEFF. Major N transporter genes, NRT1.8 and NRT3.1 were predicted for explaining variation for NUTEFF and NUPEFF, respectively. Most significant amino acid transporter gene, AAP1 appeared associated with NUE under limited N conditions. All these candidates were predicted in the regions of high linkage disequilibrium. Sequence information of the predicted candidate genes will permit development of molecular markers to aid breeding for high NUE.

中文翻译：

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芥菜氮利用效率相关参数的关联遗传学。

关键信息

全基因组关联研究允许预测与氮利用效率相关的 17 个候选基因。获得的新信息可以更好地理解印度芥菜这一性状种质变异的基因组控制。

抽象的

印度芥菜 ( Brassica juncea (L.) Czern & Coss.)的氮利用效率 (NUE)很低，大多数将 NUE 与作物性能相结合的育种工作都没有成功。潜在的遗传学也仍未被探索。我们测试了 92 个 SNP 基因分型的自交系的产量成分性状、氮吸收效率 (NUPEFF)、氮利用效率 (NUTEFF)、氮收获指数 (NHI) 和 NUE，在两个氮剂量下（N _o不添加 N 和 N ₁₀₀添加@100 公斤/公顷）。基因型 IC-2489-88、M-633、MCP-632、HUJM 1080、GR-325 和 DJ-65 在低 N 条件下记录了高 NUE。这些也显示在高 N 条件下提高作物性能。一种确定的芥菜基因型 DJ-113 DT -3 显示最大 NUTEFF。全基因组关联研究 (GWAS) 促进了 17 个数量性状基因座 (QTL) 的识别。环境特异性高。B 基因组染色体（B02、B03、B05、B07 和 B08）包含许多有用的基因座。我们还使用区域关联映射 (RAM) 来补充 GWAS 的结果。峰值 SNP 周围基因组区域的注释有助于预测根结构、N 吸收、同化和再活化的几个基因候选者。CAT9 (At1g05940 ) 一直被设想用于 NUE 和 NUPEFF。主要 N 转运蛋白基因，NRT1.8预测和NRT3.1分别用于解释 NUTEFF 和 NUPEFF 的变化。在有限的 N 条件下，最重要的氨基酸转运蛋白基因AAP1似乎与 NUE 相关。所有这些候选者都被预测在高度连锁不平衡的区域中。预测的候选基因的序列信息将允许开发分子标记以帮助高 NUE 的育种。