A two-step adaptive walk rewires nutrient transport in a challenging edaphic environment

Most well-characterized cases of adaptation involve single genetic loci. Theory suggests that multilocus adaptive walks should be common, but these are challenging to identify in natural populations. Here, we combine trait mapping with population genetic modeling to show that a two-step process rewired nutrient homeostasis in a population of Arabidopsis as it colonized the base of an active stratovolcano characterized by extremely low soil manganese (Mn). First, a variant that disrupted the primary iron (Fe) uptake transporter gene (IRT1) swept quickly to fixation in a hard selective sweep, increasing Mn but limiting Fe in the leaves. Second, multiple independent tandem duplications occurred at NRAMP1 and together rose to near fixation in the island population, compensating the loss of IRT1 by improving Fe homeostasis. This study provides a clear case of a multilocus adaptive walk and reveals how genetic variants reshaped a phenotype and spread over space and time

Dünya ıspanak genetik kolleksiyonlarının moleküler markörlerle karakterizasyonu

Thesis (Master)--Izmir Institute of Technology, Molecular Biology and Genetics., Izmir, 2015Includes bibliographical references (leaves: 28-29)Text in English; Abstract: Turkish and Englishix, 29 leavesSpinach (Spinacia oleracea L.) belongs to the Amaranthaceae family and is a popular and nutritious vegetable. It is believed that this green leafy plant originated from Persia which is now modern Iran and neighboring countries. In this study we screened 176 spinach world collection germplasm accessions with 15 known SSR markers. The markers produced 58 bands with 57 identified as polymorphic. PIC values of the markers ranged between 0.01 and 0.44. Average PIC value was 0.28. Based on allele analysis with Darwin5 and STRUCTURE tools, 176 individual were clustered into three groups. The first cluster mostly consisted of accessions from Europe and USA and contained 69 samples. The second cluster mostly consisted of lines from Asia and neighboring countries and contained 89 samples. The third cluster did not represent any characteristic according to geographic region, thus it was called an intermixed cluster which contained 18 samples. The maximum genetic dissimilarity of spinach accessions was 0.551 and minimum was 0.019. Average genetic dissimilarity was 0.217. Moreover we sequenced S. oleracea L. cv. Universal nuclear genome via IIIumina MiSeq technology and genome assembly was performed to develop new spinach–specific SSR markers. As a result, 3853 SSRs were identified in the assembled genome and we successfully designed 3275 primer pairs for these identified SSR motifs. These newly developed SSR markers will be helpful to scientists who are interested in spinach genome diversity and breeding.Ispanak (Spinacia oleracea L.) Amaranthaceae ailesine ait olan popüler ve besleyici bir sebzedir. Bu yeşil yapraklı bitkinin Persia (İran ve komşu ülkelerden) kökenlendiğine inanılır. Bu çalışmada Dünya Koleksiyonuna ait 176 ıspanak çeşidi, bilinen 15 SSR markır ile taranmıştır. Markırlar 57’si polimorfik olmak üzere 58 bant üretmiştir. Markırların PIC değerleri 0.01 ile 0.44 arasında değişmektedir. Ortalama PIC değeri ise 0.28’dir. Darwin5 ve STRUCTURE programlarının allel analizlerine göre 176 birey üç grupta toplanmıştır. Birinci grupta çoğunlukla Amerika ve Avrupa çeşitleri olmak üzere 69 örnek birey vardır. İkinci grup ise çoğunlukla Asya ve komşu ülkelerden olmak üzere 89 birey vardır. Üçüncü grup coğrafi alana göre hiç bir karakteristik göstermemiştr, bu nedenle 18 birey içeren bu grup intermixed grup olarak isimlendirilmiştir. Ispanak çeşitlerinin genetik farklılığı maksimum 0.051 ve minum 0.019’dur. Ortalama genetik farklılık ise 0.217’dir. Ayrica S. oleracea L. cv. Universal nuklear genomu IIIumina MiSeq teknolojisi kullanılarak dizilenip, ıspanak-spesifik SSR markır dizaynı için genom montajı yapıldı. Sonuç olarak, montajlanan genomda 3852 SSRs tespit edildi ve 3275 primer çifti, tespit edilen SSR motiflerine başarılı olarak dizayn edildi. Bu yeni geliştirilen SSR markırlar, ıspanak genom çeşitliliği ve ıslah konusu ile ilgilenen bilim adamlarına yardımcı olacaktır

Dünya ıspanak genetik kolleksiyonlarının moleküler markörlerle karakterizasyonu

Thesis (Master)--Izmir Institute of Technology, Molecular Biology and Genetics., Izmir, 2015Includes bibliographical references (leaves: 28-29)Text in English; Abstract: Turkish and Englishix, 29 leavesSpinach (Spinacia oleracea L.) belongs to the Amaranthaceae family and is a popular and nutritious vegetable. It is believed that this green leafy plant originated from Persia which is now modern Iran and neighboring countries. In this study we screened 176 spinach world collection germplasm accessions with 15 known SSR markers. The markers produced 58 bands with 57 identified as polymorphic. PIC values of the markers ranged between 0.01 and 0.44. Average PIC value was 0.28. Based on allele analysis with Darwin5 and STRUCTURE tools, 176 individual were clustered into three groups. The first cluster mostly consisted of accessions from Europe and USA and contained 69 samples. The second cluster mostly consisted of lines from Asia and neighboring countries and contained 89 samples. The third cluster did not represent any characteristic according to geographic region, thus it was called an intermixed cluster which contained 18 samples. The maximum genetic dissimilarity of spinach accessions was 0.551 and minimum was 0.019. Average genetic dissimilarity was 0.217. Moreover we sequenced S. oleracea L. cv. Universal nuclear genome via IIIumina MiSeq technology and genome assembly was performed to develop new spinach–specific SSR markers. As a result, 3853 SSRs were identified in the assembled genome and we successfully designed 3275 primer pairs for these identified SSR motifs. These newly developed SSR markers will be helpful to scientists who are interested in spinach genome diversity and breeding.Ispanak (Spinacia oleracea L.) Amaranthaceae ailesine ait olan popüler ve besleyici bir sebzedir. Bu yeşil yapraklı bitkinin Persia (İran ve komşu ülkelerden) kökenlendiğine inanılır. Bu çalışmada Dünya Koleksiyonuna ait 176 ıspanak çeşidi, bilinen 15 SSR markır ile taranmıştır. Markırlar 57’si polimorfik olmak üzere 58 bant üretmiştir. Markırların PIC değerleri 0.01 ile 0.44 arasında değişmektedir. Ortalama PIC değeri ise 0.28’dir. Darwin5 ve STRUCTURE programlarının allel analizlerine göre 176 birey üç grupta toplanmıştır. Birinci grupta çoğunlukla Amerika ve Avrupa çeşitleri olmak üzere 69 örnek birey vardır. İkinci grup ise çoğunlukla Asya ve komşu ülkelerden olmak üzere 89 birey vardır. Üçüncü grup coğrafi alana göre hiç bir karakteristik göstermemiştr, bu nedenle 18 birey içeren bu grup intermixed grup olarak isimlendirilmiştir. Ispanak çeşitlerinin genetik farklılığı maksimum 0.051 ve minum 0.019’dur. Ortalama genetik farklılık ise 0.217’dir. Ayrica S. oleracea L. cv. Universal nuklear genomu IIIumina MiSeq teknolojisi kullanılarak dizilenip, ıspanak-spesifik SSR markır dizaynı için genom montajı yapıldı. Sonuç olarak, montajlanan genomda 3852 SSRs tespit edildi ve 3275 primer çifti, tespit edilen SSR motiflerine başarılı olarak dizayn edildi. Bu yeni geliştirilen SSR markırlar, ıspanak genom çeşitliliği ve ıslah konusu ile ilgilenen bilim adamlarına yardımcı olacaktır

Transcriptomic analysis of boron hyperaccumulation mechanisms in Puccinellia distans

Puccinellia distans, common alkali grass, is found throughout the world and can survive in soils with boron concentrations that are lethal for other plant species. Indeed, P. distans accumulates very high levels of this element. Despite these interesting features, very little research has been performed to elucidate the boron tolerance mechanism in this species. In this study, P. distans samples were treated for three weeks with normal (0.5 mg L−1) and elevated (500 mg L−1) boron levels in hydroponic solution. Expressed sequence tags (ESTs) derived from shoot tissue were analyzed by RNA sequencing to identify genes up and down-regulated under boron stress. In this way, 3312 differentially expressed transcripts were detected, 67.7% of which were up-regulated and 32.3% of which were down-regulated in boron-treated plants. To partially confirm the RNA sequencing results, 32 randomly selected transcripts were analyzed for their expression levels in boron-treated plants. The results agreed with the expected direction of change (up or down-regulation). A total of 1652 transcripts had homologs in A. thaliana and/or O. sativa and mapped to 1107 different proteins. Functional annotation of these proteins indicated that the boron tolerance and hyperaccumulation mechanisms of P. distans involve many transcriptomic changes including: alterations in the malate pathway, changes in cell wall components that may allow sequestration of excess boron without toxic effects, and increased expression of at least one putative boron transporter and two putative aquaporins. Elucidation of the boron accumulation mechanism is important in developing approaches for bioremediation of boron contaminated soils.TUBITAK (113Z930

Newly developed SSR markers reveal genetic diversity and geographical clustering in spinach (Spinacia oleracea)

Spinach is a popular leafy green vegetable due to its nutritional composition. It contains high concentrations of vitamins A, E, C, and K, and folic acid. Development of genetic markers for spinach is important for diversity and breeding studies. In this work, Next Generation Sequencing (NGS) technology was used to develop genomic simple sequence repeat (SSR) markers. After cleaning and contig assembly, the sequence encompassed 2.5% of the 980 Mb spinach genome. The contigs were mined for SSRs. A total of 3852 SSRs were detected. Of these, 100 primer pairs were tested and 85% were found to yield clear, reproducible amplicons. These 85 markers were then applied to 48 spinach accessions from worldwide origins, resulting in 389 alleles with 89% polymorphism. The average gene diversity (GD) value of the markers (based on a GD calculation that ranges from 0 to 0.5) was 0.25. Our results demonstrated that the newly developed SSR markers are suitable for assessing genetic diversity and population structure of spinach germplasm. The markers also revealed clustering of the accessions based on geographical origin with clear separation of Far Eastern accessions which had the overall highest genetic diversity when compared with accessions from Persia, Turkey, Europe, and the USA. Thus, the SSR markers have good potential to provide valuable information for spinach breeding and germplasm management. Also they will be helpful for genome mapping and core collection establishment.Izmir Institute of Technology Scientific Research Project, IYTE-BA

Development of Simple Sequence Repeat Markers in Hazelnut (Corylus avellana L.) by Next-Generation Sequencing and Discrimination of Turkish Hazelnut Cultivars

European hazelnut (Corylus avellana) is a diploid tree species and is widely used in confections. Hazelnuts are, to a large part, produced in Turkey with the cultivar “Tombul” widely grown in the Black Sea region. In this work, the “Tombul” genome was partially sequenced by next-generation sequencing technology yielding 29.2% (111.85 Mb) of the ~ 385 Mb (1C). This sequence information was used to develop genetic markers in order to enable differentiation of material before the long maturation process and to facilitate future breeding strategies. A total of 90,142 simple sequence repeats (SSRs) were identified in the contigs giving a frequency of 1 SSR per 1240 nt in the assembly. Mononucleotides were the most abundant SSR marker type (60.9%) followed by di- and trinucleotides. Primer pairs were designed for 75,139 (83.3%) of the SSRs. Fifty SSR primers were applied to 47 hazelnut accessions from nine countries to test their effectiveness and polymorphism. The markers amplified an average of 3.2 fragments. The highest polymorphism information content value was for cavSSR11062 (0.97) and the lowest (0.04) was for cavSSR13386. Two markers were monomorphic: cavSSR12855 and cavSSR13267. Single-copy SSR primers were also assessed for their ability to discriminate 19 Turkish cultivars, and it was found that seven primer pairs (Cav4217, Cav14875, Cav14418, Cav2704, Cav12862, Cav3909, Cav1361) were sufficient for this task. Thus, this study developed new SSR markers for use in hazelnut breeding and genetic studies and also provide a method to distinguish and identify true-type Turkish cultivars.</p

Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages

Understanding how populations adapt to abrupt environmental change is necessary to predict responses to future challenges, but identifying specific adaptive variants, quantifying their responses to selection and reconstructing their detailed histories is challenging in natural populations. Here, we use Arabidopsis from the Cape Verde Islands as a model to investigate the mechanisms of adaptation after a sudden shift to a more arid climate. We find genome-wide evidence of adaptation after a multivariate change in selection pressures. In particular, time to flowering is reduced in parallel across islands, substantially increasing fitness. This change is mediated by convergent de novo loss of function of two core flowering time genes: FRI on one island and FLC on the other. Evolutionary reconstructions reveal a case where expansion of the new populations coincided with the emergence and proliferation of these variants, consistent with models of rapid adaptation and evolutionary rescue