Table_7_Comprehensive QTL analyses of nitrogen use efficiency in indica rice.XLSX

Nitrogen-use efficiency (NUE) in rice is a complex quantitative trait involved in multiple biological processes and agronomic traits; however, the genetic basis and regulatory network of NUE remain largely unknown. We constructed a high-resolution microarray-based genetic map for 261 recombinant inbred lines derived from two indica parents. Using 2,345 bin markers, comprehensive analyses of quantitative trait loci (QTLs) of seven key agronomic traits under two different N levels were performed. A total of 11 non-redundant QTLs for effective panicle number (EPN), 7 for grain number per panicle, 13 for thousand-grain weight, 2 for seed-setting percentage, 15 for plant height, 12 for panicle length, and 6 for grain yield per plant were identified. The QTL regions were as small as 512 kb on average, and more than half spanned an interval smaller than 100 kb. Using this advantage, we identified possible candidate genes of two major EPN-related QTLs. One QTL detected under both N levels possibly encodes a DELLA protein SLR1, which is known to regulate NUE, although the natural variations of this protein have not been reported. The other QTL detected only under a high N level could encode the transcription factor OsbZIP59. We also predicted the possible candidate genes for another three of the NUE-related QTLs. Our results provide a reference for improving NUE-related QTL cloning and promote our understanding of NUE regulation in indica rice.

水稻的氮利用效率（Nitrogen-use efficiency, NUE）是一类参与多种生物学过程及农艺性状调控的复杂数量性状，但其遗传基础与调控网络仍有大量未知之处。本研究针对由两个籼稻亲本衍生的261个重组自交系，构建了基于微阵列的高分辨率遗传图谱。借助2345个Bin标记（bin markers），对两种不同氮水平下7个关键农艺性状的数量性状位点（quantitative trait loci, QTLs）开展了全面分析。最终共鉴定到11个与有效穗数（effective panicle number, EPN）相关的非冗余QTL、7个每穗粒数相关QTL、13个千粒重相关QTL、2个结实率相关QTL、15个株高相关QTL、12个穗长相关QTL以及6个单株产量相关QTL。这些QTL的区间平均长度仅为512千碱基对，超过一半的区间跨度小于100千碱基对。依托这一优势，我们鉴定出两个与有效穗数相关的主效QTL的潜在候选基因：其中一个在两种氮水平下均能检测到的QTL，其编码的DELLA蛋白SLR1已知可调控氮利用效率，尽管该蛋白的自然变异尚未见报道；另一个仅在高氮水平下检测到的QTL，则可能编码转录因子OsbZIP59。此外，我们还对另外3个与氮利用效率相关的QTL进行了候选基因预测。本研究结果为克隆氮利用效率相关QTL提供了重要参考，同时也加深了我们对籼稻氮利用效率调控机制的理解。