Patatesde (Solanum tuberosum L.) kurağa tepki veren transpozonların ve transkripsiyon faktörlerin in siliko analizi

Patates (Solanum tuberosum L.) tahıl grubundan olmayan önemli bir kültür bitkisidir ve küresel gıda güvenliği açısından büyük bir öneme sahiptir. Kuraklık, tarımsal üretimde büyük verim kayıplarına neden olan başlıca abiyotik stres faktörlerinden biridir ve patatesde yumru oluşumu, yumru verimi ve yumruların kalitesini olumsuz yönde etkilemektedir. Birçok ökaryotik türdeki genomun büyük bir bölümünü hareketli elementler oluşturmaktadır. Transpozon elementlerin (TE) stres altında nasıl aktive olduklarının moleküler mekanızması birçok çalışmada tanımlamıştır. Stres ve çevresel zorlukların, özellikle bitkilerde hareketli elementlerin ekspresyonunu veya transpozisyonunu uyardığı bilinmektedir. Strese tepki veren bu genlerin transkripsiyonu büyük ölçüde transkripsiyon faktörleri tarafından kontrol edilmektedir. Son yıllarda, bitkilerin kurağa tepkilerinin düzenlenmesinde önemli role sahip bazı transkripsiyon faktörleri belirlenmiştir. Bu çalışmada, transkripsiyon homolojisi ve anotasyon yaklaşımı kullanılarak yumru büyütme dönemindeki patateste kuraklığa tepki veren hareketli elementler ve transkripsiyon faktörü aileleri tanımlanmıştır. Sonuçlarımız, hareketli elementlerin alt aileleri için okuma sayılarının DNA ve RNA transpozonları arasında farklı dağılımlar sağladığını ve bHLH, WRKY, NAC, AP2/ERF transkripsiyon faktörlerini kodlayan çok sayıda genin, kuraklık stresine tepkinin düzenlenmesinde önemli işlevlere sahip olabileceğini göstermiştir. Strese tepkide yer alan hareketli elementlerin ve transkripsiyon faktörlerin tanımlanması ve bunların beraber değerlendirilmesi, işlevsel genomik çalışmaları ve strese dirençli bitkilerin geliştirilmesinde yeni ıslah stratejilerinin tasarlanması için yararlı bilgiler sağlayabilir.

Anahtar Kelimeler:

Kuraklık, Patates, Transkripsiyon, Transpozon, Transkripsiyon faktör

In silico analysis of drought responsive transposons and transcription factors in Solanum tuberosum L.

Potato (Solanum tuberosum L.) is the most important non-grainfood crop and is essential for global food security. Drought is one of the major abiotic stress factors resulting in huge yield loss in the production of crops and similarly, it negativelly affects the tuberization, tuber yield and tuber quality of potato. Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Several studies have identified the molecular mechanism that cause the activation of TEs under stress. Stresses and environmental challenges, in particular, are known to alter the expression or stimulate the transposition of mobile elements in plants. Transcription of these stress-responsive genes is largely controlled by transcription factors (TFs). A number of transcription factors playing an essential role in drought tolerance of plants have been identified in the past few years. In this work, a subset of drought responsive TE families and TFs in potato at tuber bulking stage was defined, based on genome-wide transposon homology and annotation. Our results indicated that, the read numbers for TE subfamilies yielded different distributions between DNA and RNA transposons. In addition, many TFs such as bHLH, WRKY, NAC, AP2/ERF may have important functions in regulation of drought tolerance in potato. Identification of TEs and TFs which are taking part in stress can offer useful information for functional genomics and designing novel breeding strategies for developing stress tolerant plants.

Keywords:

Drought, Potato, Transcription, Transposon, Transcription factor,

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