Table_1.DOC

<p>Seed germination plays important roles in the establishment of seedlings and their subsequent growth; however, seed germination is inhibited by salinity, and the inhibitory mechanism remains elusive. Our results indicate that NaCl treatment inhibits rice seed germination by decreasing the contents of bioactive gibberellins (GAs), such as GA₁ and GA_4, and that this inhibition can be rescued by exogenous bioactive GA application. To explore the mechanism of bioactive GA deficiency, the effect of NaCl on GA metabolic gene expression was investigated, revealing that expression of both GA biosynthetic genes and GA-inactivated genes was up-regulated by NaCl treatment. These results suggest that NaCl-induced bioactive GA deficiency is caused by up-regulated expression of GA-inactivated genes, and the up-regulated expression of GA biosynthetic genes might be a consequence of negative feedback regulation of the bioactive GA deficiency. Moreover, we provide evidence that NaCl-induced bioactive GA deficiency inhibits rice seed germination by decreasing α-amylase activity via down-regulation of α-amylase gene expression. Additionally, exogenous bioactive GA rescues NaCl-inhibited seed germination by enhancing α-amylase activity. Thus, NaCl treatment reduces bioactive GA content through promotion of bioactive GA inactivation, which in turn inhibits rice seed germination by decreasing α-amylase activity via down-regulation of α-amylase gene expression.</p

Table_2_A SNP-Based Linkage Map Revealed QTLs for Resistance to Early and Late Leaf Spot Diseases in Peanut (Arachis hypogaea L.).DOCX

<p>Cultivated peanut (Arachis hypogaea L.) is an important oilseed crop that is grown extensively in Africa, Asia and America. The diseases early and late leaf spot severely constrains peanut production worldwide. Because multiple genes control resistance to leaf spot diseases, conventional breeding is a time-consuming approach for pyramiding resistance genes into a single genotype. Marker-assisted selection (MAS) would complement and accelerate conventional breeding once molecular markers tightly associated with the resistance genes are identified. In this study, we have generated a large number of SNPs through genotyping by sequencing (GBS) and constructed a high-resolution map with an average distance of 1.34 cM among 2,753 SNP markers distributed on 20 linkage groups. QTL mapping has revealed that major QTL within a confidence interval could provide an efficient way to detect putative resistance genes. Analysis of the interval sequences has indicated that a major QTL for resistance to late leaf spot anchored by two NBS-LRR resistance genes on chromosome B05. Two major QTLs located on chromosomes A03 and B04 were associated with resistance genes for early leaf spot. Sequences within the confidence interval would facilitate identifying resistance genes and applying marker-assisted selection for resistance.</p

Table_1_A SNP-Based Linkage Map Revealed QTLs for Resistance to Early and Late Leaf Spot Diseases in Peanut (Arachis hypogaea L.).DOCX

<p>Cultivated peanut (Arachis hypogaea L.) is an important oilseed crop that is grown extensively in Africa, Asia and America. The diseases early and late leaf spot severely constrains peanut production worldwide. Because multiple genes control resistance to leaf spot diseases, conventional breeding is a time-consuming approach for pyramiding resistance genes into a single genotype. Marker-assisted selection (MAS) would complement and accelerate conventional breeding once molecular markers tightly associated with the resistance genes are identified. In this study, we have generated a large number of SNPs through genotyping by sequencing (GBS) and constructed a high-resolution map with an average distance of 1.34 cM among 2,753 SNP markers distributed on 20 linkage groups. QTL mapping has revealed that major QTL within a confidence interval could provide an efficient way to detect putative resistance genes. Analysis of the interval sequences has indicated that a major QTL for resistance to late leaf spot anchored by two NBS-LRR resistance genes on chromosome B05. Two major QTLs located on chromosomes A03 and B04 were associated with resistance genes for early leaf spot. Sequences within the confidence interval would facilitate identifying resistance genes and applying marker-assisted selection for resistance.</p

Comparative analysis of NBS-LRR genes and their response to <i>Aspergillus flavus</i> in <i>Arachis</i>

<div><p>Studies have demonstrated that nucleotide-binding site–leucine-rich repeat (NBS–LRR) genes respond to pathogen attack in plants. Characterization of NBS–LRR genes in peanut is not well documented. The newly released whole genome sequences of <i>Arachis duranensis</i> and <i>Arachis ipaënsis</i> have allowed a global analysis of this important gene family in peanut to be conducted. In this study, we identified 393 (AdNBS) and 437 (AiNBS) NBS–LRR genes from <i>A</i>. <i>duranensis</i> and <i>A</i>. <i>ipaënsis</i>, respectively, using bioinformatics approaches. Full-length sequences of 278 AdNBS and 303 AiNBS were identified. Fifty-one orthologous, four AdNBS paralogous, and six AiNBS paralogous gene pairs were predicted. All paralogous gene pairs were located in the same chromosomes, indicating that tandem duplication was the most likely mechanism forming these paralogs. The paralogs mainly underwent purifying selection, but most LRR 8 domains underwent positive selection. More gene clusters were found in <i>A</i>. <i>ipaënsis</i> than in <i>A</i>. <i>duranensis</i>, possibly owing to tandem duplication events occurring more frequently in <i>A</i>. <i>ipaënsis</i>. The expression profile of NBS–LRR genes was different between <i>A</i>. <i>duranensis</i> and <i>A</i>. <i>hypogaea</i> after <i>Aspergillus flavus</i> infection. The up-regulated expression of NBS–LRR in <i>A</i>. <i>duranensis</i> was continuous, while these genes responded to the pathogen temporally in <i>A</i>. <i>hypogaea</i>.</p></div

NBS-LRR gene number and cluster number in <i>A</i>. <i>duranensis</i> and <i>A</i>. <i>ipaënsis</i>.

<p>A and B represent gene number in <i>A</i>. <i>duranensis</i> and <i>A</i>. <i>ipaënsis</i>, respectively. C and D represent cluster number in <i>A</i>. <i>duranensis</i> and <i>A</i>. <i>ipaënsis</i>, respectively.</p

Chromosomal location and homologous gene relationship of NBS-LRR genes from <i>A</i>. <i>duranensis</i> and <i>A</i>. <i>ipaënsis</i>.

<p>The letters and numbers outside the circle represent species and chromosomes, respectively. A and B represent <i>A</i>. <i>duranensis</i> and <i>A</i>. <i>ipaënsis</i>, respectively.</p

Comparison of K_a/K_s values among NBS-LRR sequence, NBS and LRR regions.

<p>A, B and C represent NBS-LRR sequence, NBS and LRR regions, respectively.</p

Expression of NBS-LRR genes from <i>A</i>. <i>duranensis</i> and <i>A</i>. <i>hypogaea</i> after <i>A</i>. <i>flavus</i> infection.

<p>The Y-axis indicates the relative expression level; X-axis indicates days of <i>A</i>. <i>flavus</i> infection. The standard errors are plotted using vertical lines.</p

Phylogenetic tree of NBS-LRR from <i>A</i>. <i>duranensis</i> and <i>A</i>. <i>ipaënsis</i>.

<p>The phylogenetic tree was generated using CNL and TNL full-length proteins from <i>A</i>. <i>duranensis</i> and <i>A</i>. <i>ipaënsis</i> using MEGA 6.0 by the maximum likelihood (ML) with Jones-Taylor-Thornton model based on 1,000 bootstrap replicates.</p

Leaves of resistant Yuanza 9102 (WT) and susceptible mutant (M14) response to late leaf spot infection.

<p>Leaves of resistant Yuanza 9102 (WT) and susceptible mutant (M14) response to late leaf spot infection.</p