Allelic characterization and protein structure analysis reveals the involvement of splice site mutation for growth habit differences in Lablab purpureus (L.) Sweet.
Allelic characterization and protein structure analysis reveals the involvement of splice site mutation for growth habit differences in Lablab purpureus (L.) Sweet.
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DOI：
10.1186/s43141-021-00136-z
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发表时间：
2021-02-22
期刊：
影响因子：
--
通讯作者：
Patel R
中科院分区：
文献类型：
--
作者：
Kaldate S;Patel A;Modha K;Parekh V;Kale B;Vadodariya G;Patel R
生长习性与开花的相互关系在豆类驯化历史中起着关键作用；然而，在印度豆中还没有发现负责这些特征的实际基因。确定的生长习性是可取的，因为它开花早，光不敏感，豆荚同步成熟，易于人工采收和作物周期短。本研究旨在通过候选基因方法，结合测序、多序列比对、蛋白结构预测和结合口袋分析，鉴定、表征和验证与生长习惯有关的基因。利用从普通豆PvTFL1y位点设计的引物，从GPKH 120（不确定）和GNIB-21（确定）中扩增出末端开花位点。基因预测显示，这两个等位基因的第三和第四个外显子的长度不同。等位基因序列比较表明，GNIB 21的第三外显子末端由鸟嘌呤转变为腺嘌呤。该剪接位点单核苷酸多态性（SNP）通过测序在种质系中得到验证。蛋白质结构分析表明，末端开花位点（TFL）蛋白与其他蛋白相互作用涉及两个结合袋。在确定基因型GNIB 21中，位于TFL位点第三外显子末端的剪接位点SNP负责茎尖分生组织向生殖命运的转化。剪接位点SNP导致GNIB 21突变体TFL蛋白缺失14个氨基酸，使该蛋白无功能。这种缺失干扰了先前报道的阴离子结合口袋和次级结合口袋，因为小β-片从外部环位移。这一发现可能使通过基因组编辑来调节印度豆和其他豆类作物的生长习惯成为可能。
Interrelationship between growth habit and flowering played a key role in the domestication history of pulses; however, the actual genes responsible for these traits have not been identified in Indian bean. Determinate growth habit is desirable due to its early flowering, photo-insensitivity, synchronous pod maturity, ease in manual harvesting and short crop duration. The present study aimed to identify, characterize and validate the gene responsible for growth habit by using a candidate gene approach coupled with sequencing, multiple sequence alignment, protein structure prediction and binding pocket analysis. Terminal flowering locus was amplified from GPKH 120 (indeterminate) and GNIB-21 (determinate) using the primers designed from PvTFL1y locus of common bean. Gene prediction revealed that the length of the third and fourth exons differed between the two alleles. Allelic sequence comparison indicated a transition from guanine to adenine at the end of the third exon in GNIB 21. This splice site single-nucleotide polymorphism (SNP) was validated in germplasm lines by sequencing. Protein structure analysis indicated involvement of two binding pockets for interaction of terminal flowering locus (TFL) protein with other proteins. The splice site SNP present at the end of the third exon of TFL locus is responsible for the transformation of shoot apical meristem into a reproductive fate in the determinate genotype GNIB 21. The splice site SNP leads to absence of 14 amino acids in mutant TFL protein of GNIB 21, rendering the protein non-functional. This deletion disturbed previously reported anion-binding pocket and secondary binding pocket due to displacement of small β-sheet away from an external loop. This finding may enable the modulation of growth habit in Indian bean and other pulse crops through genome editing.
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影响因子：
4.6
作者：
Kawamoto N;Sasabe M;Endo M;Machida Y;Araki T
通讯作者：
Araki T
影响因子：
2.9
作者：
Benkert, Pascal;Tosatto, Silvio C. E.;Schwede, Torsten
通讯作者：
Schwede, Torsten
势在必行的未充分开发的豆科植物育种的发展和前景：回顾。
影响因子：
5.6
作者：
Dhaliwal SK;Talukdar A;Gautam A;Sharma P;Sharma V;Kaushik P
通讯作者：
Kaushik P
保守的CO-FT调节子有助于大豆光周期开花控制
影响因子：
5.3
作者：
Fan C;Hu R;Zhang X;Wang X;Zhang W;Zhang Q;Ma J;Fu YF
通讯作者：
Fu YF
DOI：
10.21273/jashs.121.5.794
发表时间：
1996-09-01
影响因子：
1.9
作者：
Jung, GW;Coyne, DP;Kaeppler, SM
通讯作者：
Kaeppler, SM