Gelli Malleswari, Konda Anji Reddy, Liu Kan, Zhang Chi, Clemente Thomas E, Holding David R, Dweikat Ismail M
Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA.
BMC Plant Biol. 2017 Jul 11;17(1):123. doi: 10.1186/s12870-017-1064-9.
Quantitative trait loci (QTLs) detected in one mapping population may not be detected in other mapping populations at all the time. Therefore, before being used for marker assisted breeding, QTLs need to be validated in different environments and/or genetic backgrounds to rule out statistical anomalies. In this regard, we mapped the QTLs controlling various agronomic traits in a recombinant inbred line (RIL) population in response to Nitrogen (N) stress and validated these with the reported QTLs in our earlier study to find the stable and consistent QTLs across populations. Also, with Illumina RNA-sequencing we checked the differential expression of gene (DEG) transcripts between parents and pools of RILs with high and low nitrogen use efficiency (NUE) and overlaid these DEGs on to the common validated QTLs to find candidate genes associated with N-stress tolerance in sorghum.
An F RIL population derived from a cross between CK60 (N-stress sensitive) and San Chi San (N-stress tolerant) inbred sorghum lines was used to map QTLs for 11 agronomic traits tested under different N-levels. Composite interval mapping analysis detected a total of 32 QTLs for 11 agronomic traits. Validation of these QTLs revealed that of the detected, nine QTLs from this population were consistent with the reported QTLs in earlier study using CK60/China17 RIL population. The validated QTLs were located on chromosomes 1, 6, 7, 8, and 9. In addition, root transcriptomic profiling detected 55 and 20 differentially expressed gene (DEG) transcripts between parents and pools of RILs with high and low NUE respectively. Also, overlay of these DEG transcripts on to the validated QTLs found candidate genes transcripts for NUE and also showed the expected differential expression. For example, DEG transcripts encoding Lysine histidine transporter 1 (LHT1) had abundant expression in San Chi San and the tolerant RIL pool, whereas DEG transcripts encoding seed storage albumin, transcription factor IIIC (TFIIIC) and dwarfing gene (DW2) encoding multidrug resistance-associated protein-9 homolog showed abundant expression in CK60 parent, similar to earlier study.
The validated QTLs among different mapping populations would be the most reliable and stable QTLs across germplasm. The DEG transcripts found in the validated QTL regions will serve as future candidate genes for enhancing NUE in sorghum using molecular approaches.
在一个作图群体中检测到的数量性状基因座（QTL）并非在所有情况下都能在其他作图群体中被检测到。因此，在用于标记辅助育种之前，需要在不同环境和/或遗传背景下对QTL进行验证，以排除统计异常。在这方面，我们对一个重组自交系（RIL）群体中响应氮（N）胁迫的控制各种农艺性状的QTL进行了定位，并将其与我们早期研究中报道的QTL进行验证，以找到不同群体间稳定且一致的QTL。此外，我们利用Illumina RNA测序技术检测了高氮利用效率（NUE）和低氮利用效率的RIL亲本与混合池之间基因（DEG）转录本的差异表达，并将这些DEG叠加到共同验证的QTL上，以寻找与高粱耐N胁迫相关的候选基因。
利用从CK60（N胁迫敏感）和三尺三（N胁迫耐受）自交高粱品系杂交得到的F RIL群体，对不同N水平下测试的11个农艺性状进行QTL定位。复合区间作图分析共检测到11个农艺性状的32个QTL。对这些QTL的验证表明，在检测到的QTL中，该群体中的9个QTL与早期使用CK60/中国17 RIL群体的研究中报道的QTL一致。验证的QTL位于第1、6、7、8和9号染色体上。此外，根系转录组分析分别在高NUE和低NUE的RIL亲本与混合池之间检测到55个和20个差异表达基因（DEG）转录本。此外，将这些DEG转录本叠加到验证的QTL上，发现了NUE的候选基因转录本，并显示出预期的差异表达。例如，编码赖氨酸组氨酸转运蛋白1（LHT1）的DEG转录本在三尺三和耐胁迫RIL混合池中表达丰富，而编码种子贮藏白蛋白、转录因子IIIC（TFIIIC）和编码多药耐药相关蛋白9同源物的矮化基因（DW2）的DEG转录本在CK60亲本中表达丰富，与早期研究相似。
不同作图群体间验证的QTL将是整个种质中最可靠和稳定的QTL。在验证的QTL区域中发现的DEG转录本将作为未来利用分子方法提高高粱NUE的候选基因。
