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(searched for: doi:10.1007/s00122-017-2932-2)
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, Atta Ur Rahman, Abdul Rehman
Rice Research for Quality Improvement: Genomics and Genetic Engineering pp 437-464; doi:10.1007/978-981-15-4120-9_19

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Published: 23 October 2020
Agronomy, Volume 10; doi:10.3390/agronomy10111629

Abstract:
International genebanks have a collection of over 760 K conserved accessions of various plants, most of these accessions are within the multi-lateral system governed by the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA). However, in spite of the success in collection and conservation, only a small portion of the genetic diversity has been used in crop breeding programs. As climate change-induced new or enhanced constraints seriously hamper crop productions, researchers and breeders should be able to swiftly choose an appropriate set of genetic resources from the genebank and use them for improving crop varieties. Here, we present some advanced technologies that can effectively promote the use of diverse rice accessions held at national/international genebanks. High throughput phenotyping using multispectral imaging systems and unmanned aerial vehicles (UAV) can quickly screen large numbers of accessions for various useful traits. Such data, when combined with that from the digital rice genebank consisting of genome sequencing data, will significantly increase the efficiency in breeding efforts. Recent genome sequencing data of the rice wild species will also add to the resources available for pre-breeding efforts such as the introgression of useful genes into modern rice varieties. We expect that these advanced technologies and strategies developed through the global rice research programs will be applicable for many closely related species as well.
Agnieszka Deja-Muylle, Boris Parizot, Hans Motte,
Journal of Experimental Botany, Volume 71, pp 2379-2389; doi:10.1093/jxb/eraa029

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Dev Paudel, Smit Dhakal, Saroj Parajuli, Laxman Adhikari, Ze Peng, You Qian, Dipendra Shahi, Muhsin Avci, Shiva O. Makaju, Baskaran Kannan
Plant Life Under Changing Environment pp 917-965; doi:10.1016/b978-0-12-818204-8.00048-5

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BMC Plant Biology, Volume 19, pp 1-18; doi:10.1186/s12870-019-2203-2

Abstract:
Background Zinc (Zn) deficiency is one of the most widespread soil constraints affecting rice productivity, but the molecular mechanisms underlying the regulation of Zn deficiency response is still limited. Here, we aim to understand the molecular mechanisms of Zn deficiency response by integrating the analyses of the global miRNA and mRNA expression profiles under Zn deficiency and resupply in rice seedlings by integrating Illumina’s high-throughput small RNA sequencing and transcriptome sequencing. Results The transcriptome sequencing identified 360 genes that were differentially expressed in the shoots and roots of Zn-deficient rice seedlings, and 97 of them were recovered after Zn resupply. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply. The integrated analyses of miRNAome and transcriptome data showed that 12 differentially expressed genes are the potential target genes of 10 Zn-responsive miRNAs such as miR171g-5p, miR397b-5p, miR398a-5p and miR528-5p. Some miRNA genes and differentially expressed genes were selected for validation by quantitative RT-PCR, and their expressions were similar to that of the sequencing results. Conclusion These results provide insights into miRNA-mediated regulatory pathways in Zn deficiency response, and provide candidate genes for genetic improvement of Zn deficiency tolerance in rice.
International Journal of Molecular Sciences, Volume 20; doi:10.3390/ijms20235915

Abstract:
Soybean is an excellent source of vegetable protein and edible oil. Understanding the genetic basis of protein and oil content will improve the breeding programs for soybean. Linkage analysis and genome-wide association study (GWAS) tools were combined to detect quantitative trait loci (QTL) that are associated with protein and oil content in soybean. Three hundred and eight recombinant inbred lines (RILs) containing 3454 single nucleotide polymorphism (SNP) markers and 200 soybean accessions, including 94,462 SNPs and indels, were applied to identify QTL intervals and significant SNP loci. Intervals on chromosomes 1, 15, and 20 were correlated with both traits, and QTL qPro15-1, qPro20-1, and qOil5-1 reproducibly correlated with large phenotypic variations. SNP loci on chromosome 20 that overlapped with qPro20-1 were reproducibly connected to both traits by GWAS (p < 10−4). Twenty-five candidate genes with putative roles in protein and/or oil metabolisms within two regions (qPro15-1, qPro20-1) were identified, and eight of these genes showed differential expressions in parent lines during late reproductive growth stages, consistent with a role in controlling protein and oil content. The new well-defined QTL should significantly improve molecular breeding programs, and the identified candidate genes may help elucidate the mechanisms of protein and oil biosynthesis.
Jae-Sung Lee, , Oscar B. Zamora,
Published: 1 September 2018
Rice Science, Volume 25, pp 293-296; doi:10.1016/j.rsci.2018.08.004

Abstract:
Zinc (Zn) deficiency is a major soil constraint limiting rice crop growth and yield, yet the genetic control of tolerance mechanisms is still poorly understood. Here, we presented promising loci and candidate genes conferring tolerance to Zn deficiency and identified through association analysis using a 365 K single nucleotide polymorphism (SNP) marker array in a diverse aus (semi-wild type rice) panel. Tolerant accessions exhibited higher growth rate with relatively rare stress symptoms. Two loci on chromosomes 7 and 9 were strongly associated with plant vigor under Zn deficiency at a peak-stress stage. Based on previous microarray data from the same experimental plots, we highlighted four candidate genes whose expressions were accompanied by significant genotype and/or environment effects under Zn deficiency. Network-gene ontology supported known tolerance mechanisms, such as ascorbic acid pathway, and also suggested the importance of photosynthesis genes to overcome Zn deficiency symptoms.
Feifei Ma, Yunfeng Xu, Zhengqiang Ma, Lihui Li,
Published: 28 June 2018
Molecular Breeding, Volume 38; doi:10.1007/s11032-018-0837-7

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Published: 10 November 2017
by Wiley
Plant, Cell & Environment, Volume 40, pp 3018-3030; doi:10.1111/pce.13069

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