Transcriptional Reprogramming and Allelic Variation in Pleiotropic QTL Regulates Days to Flowering and Growth Habit in Pigeonpea

IF 6 1区 生物学 Q1 PLANT SCIENCES Plant, Cell & Environment Pub Date : 2024-12-20 DOI:10.1111/pce.15322
Kuldeep Kumar, Kumar Durgesh, Priyanka Anjoy, Harsha Srivastava, Kishor U. Tribhuvan, Amitha Mithra Sevanthi, Anupam Singh, Ratna Prabha, Sandhya Sharma, Rekha Joshi, Pradeep Kumar Jain, Nagendra Kumar Singh, Kishor Gaikwad
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Abstract

The present study investigated the linkage between days to flowering (DTF) and growth habit (GH) in pigeonpea using QTL mapping, QTL-seq, and GWAS approaches. The linkage map developed here is the largest to date, spanning 1825.56 cM with 7987 SNP markers. In total, eight and four QTLs were mapped for DTF and GH, respectively, harbouring 78 pigeonpea orthologs of Arabidopsis flowering time genes. Corroboratively, QTL-seq analysis identified a single linked QTL for both traits on chromosome 3, possessing 15 genes bearing genic variants. Together, these 91 genes were clustered primarily into autonomous, photoperiod, and epigenetic pathways. Further, we identified 39 associations for DTF and 111 associations for GH through GWAS in the QTL regions. Of these, nine associations were consistent and constituted nine haplotypes (five late, two early, one each for super-early and medium duration). The involvement of multiple genes explained the range of allelic effects and the presence of multiple LD blocks. Further, the linked QTL on chromosome 3 was fine-mapped to the 0.24-Mb region with an LOD score of 8.56, explaining 36.47% of the phenotypic variance. We identified a 10-bp deletion in the first exon of TFL1 gene of the ICPL 20338 variety, which may affect its interaction with the Apetala1 and Leafy genes, resulting in determinate GH and early flowering. Further, the genic marker developed for the deletion in the TFL1 gene could be utilized as a foreground marker in marker-assisted breeding programmes to develop early-flowering pigeonpea varieties.

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多效性QTL的转录重编程和等位基因变异调控鸽豆的开花期和生长习性。
本研究采用QTL定位、QTL-seq和GWAS方法研究了鸽子豌豆开花日数(DTF)和生长习性(GH)之间的连锁关系。这是迄今为止最大的连锁图谱,全长1825.56 cM,有7987个SNP标记。共定位到8个DTF和4个GH的qtl,包含78个拟南芥开花时间基因的鸽豌豆同源基因。QTL-seq分析在3号染色体上发现了两个性状的单个连锁QTL,具有15个携带基因变异的基因。总之,这91个基因主要聚集在自主、光周期和表观遗传途径中。此外,我们通过GWAS在QTL区域确定了39个DTF关联和111个GH关联。其中9个关联是一致的,构成9个单倍型(5个晚,2个早,超早和中早各1个)。多个基因的参与解释了等位基因效应的范围和多个LD块的存在。此外,3号染色体上的连锁QTL被精细定位到0.24 mb区域,LOD评分为8.56,解释了36.47%的表型变异。我们在ICPL 20338品种的TFL1基因的第一个外显子上发现了一个10 bp的缺失,这可能影响了它与aptala1和Leafy基因的相互作用,导致生长激素确定和开花提前。此外,开发的TFL1基因缺失基因标记可以作为标记辅助育种计划的前景标记,以开发早花鸽豆品种。
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来源期刊
Plant, Cell & Environment
Plant, Cell & Environment 生物-植物科学
CiteScore
13.30
自引率
4.10%
发文量
253
审稿时长
1.8 months
期刊介绍: Plant, Cell & Environment is a premier plant science journal, offering valuable insights into plant responses to their environment. Committed to publishing high-quality theoretical and experimental research, the journal covers a broad spectrum of factors, spanning from molecular to community levels. Researchers exploring various aspects of plant biology, physiology, and ecology contribute to the journal's comprehensive understanding of plant-environment interactions.
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