Construction of rice chromosome segment substitution lines harboring &lt;i&gt;Oryza barthii&lt;/i&gt; genome and evaluation of yield-related traits

Bessho-Uehara, Kanako; Furuta, Tomohisa; Masuda, Kengo; Yamada, Shuto; Angeles‐Shim, Rosalyn B.; Ashikari, Motoyuki; Takashi, Tomonori

doi:10.1270/jsbbs.17022

Cited by 27 publications

(21 citation statements)

References 36 publications

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“…Several methods can be used to increase or broaden the genetic base of tomatoes. These methods include, among others, advanced backcross QTL analysis [100], chromosome segments substitution lines (CSSL) [101,102], backcross inbred lines (BIL), and introgression lines (ILs), which have the common feature of developing lines carrying small pieces of donor parent chromosomes, increasing the chances to break linkage drag. These techniques combine QTL analysis with development of superior lines, which can be advanced in varieties release pipeline.…”

Section: Better Exploitation Of Tomato Genetic Resource For Heat Tolementioning

confidence: 99%

Accelerating Breeding for Heat Tolerance in Tomato (Solanum lycopersicum L.): An Integrated Approach

et al. 2019

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Heat stress is a major limiting factor for crop productivity. Tomato is highly sensitive to heat stress, which can result in a total yield loss. To adapt to current and future heat stress, there is a dire need to develop heat tolerant cultivars. Here, we review recent attempts to improve screening for heat tolerance and to exploit genetic and genomic resources in tomatoes. We provide key factors related to phenotyping environments and traits (morphological, physiological, and metabolic) to be considered to identify and breed thermo-tolerant genotypes. There is significant variability in tomato germplasm that can be harnessed to breed for thermo-tolerance. Based on our review, we propose that the use of advanced backcross populations and chromosome segments substitution lines is the best means to exploit variability for heat tolerance in non-cultivated tomato species. We applied a meta quantitative trait loci (MQTL) analysis on data from four mapping experiments to co-localize QTL associated with heat tolerance traits (e.g., pollen viability, number of pollen, number of flowers, style protrusion, style length). The analysis revealed 13 MQTL of which 11 were composed of a cluster of QTL. Overall, there was a reduction of about 1.5-fold in the confidence interval (CI) of the MQTL (31.82 cM) compared to the average CI of individual QTL (47.4 cM). This confidence interval is still large and additional mapping resolution approaches such as association mapping and multi-parent linkage mapping are needed. Further investigations are required to decipher the genetic architecture of heat tolerance surrogate traits in tomatoes. Genomic selection and new breeding techniques including genome editing and speed breeding hold promise to fast-track development of improved heat tolerance and other farmer- and consumer-preferred traits in tomatoes.

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Section: Better Exploitation Of Tomato Genetic Resource For Heat Tolementioning

confidence: 99%

Accelerating Breeding for Heat Tolerance in Tomato (Solanum lycopersicum L.): An Integrated Approach

et al. 2019

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“…CSSLs are ideal for mapping genetic population for the elimination of most genetic background noise and dissection of QTLs into the single Mendelian factor (Xu et al 2010). Although development of CSSLs is laborious and time-consuming, more and more CSSLs have been developed for their significant advantages (Bessho-Uehara et al 2017; Furuta et al 2014; Hao et al 2006; Kubo et al 2002; Qiao et al 2016; Shim et al 2010; Yoshimura 1997).…”

Section: Introductionmentioning

confidence: 99%

Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

Zhang

Shang

Ruan

et al. 2019

Rice

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Background Detecting and mapping chromosomal regions that are related to quantitative phenotypic variation in chromosome segment substitution lines (CSSLs) provides an effective means to characterize the genetic basis of complex agronomic trait. CSSLs are also powerful tools for studying the effects of quantitative trait loci (QTLs) pyramiding and interaction on phenotypic variation. Results Here, we developed three sets of CSSLs consisting of 81, 55, and 61 lines, which were derived from PA64s × 9311, Nipponbare × 9311 and PA64s × Nipponbare crosses, respectively. All of the 197 CSSLs were subjected to high-throughput genotyping by whole-genome resequencing to obtain accurate physical maps for the 3 sets of CSSLs. The 3 sets of CSSLs were used to analyze variation for 11 major agronomic traits in Hangzhou and Shenzhen and led to the detection of 71 QTLs with phenotypic effect that ranged from 7.6% to 44.8%. Eight QTLs were commonly detected under two environments for the same phenotype, and there were also 8 QTL clusters that were found. Combined with GWAS on grain length and expression profiles on young panicle tissues, qGL1 detected in CSSLs was fine mapped within a 119 kb region on chromosome 1 and LOC_Os01g53140 and LOC_Os01g53250 were the two most likely candidate genes. Conclusions Our results indicate that developing CSSLs genotyped by whole-genome resequencing are powerful tools for basic genetic research and provide a platform for the rational design of rice breeding. Meanwhile, the conjoint analysis of different CSSLs, natural population and expression profiles can facilitate QTL fine mapping. Electronic supplementary material The online version of this article (10.1186/s12284-019-0293-y) contains supplementary material, which is available to authorized users.

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“…These secondary mapping populations are required to facilitate more comprehensive analysis of target QTLs (Yano, 2001). More recently in rice, multi-parent populations called multi-parent advanced generation intercross (MAGIC; Bandillo et al, 2013), CSSLs (Bessho-Uehara et al, 2017;Ogawa et al, 2016) and nested-association mapping populations (Fragoso et al, 2017) have been used for QTL mapping.…”

Section: Approaches To Qtl Mappingmentioning

confidence: 99%

Association mapping in rice: basic concepts and perspectives for molecular breeding

Verdeprado

Kretzschmar

Begum

et al. 2018

Plant Production Science

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In the last decade, association mapping (AM) has become a well-established method to detect genes and quantitative trait loci (QTLs) associated with agronomically important traits. The identification of a large number of single nucleotide polymorphisms (SNPs) from genome sequencing and concurrent development of high-throughput genotyping platforms has led to AM being widely used for a range of crops. These technologies have been used in rice (Oryza sativa) to explore the abundant diversity and there is enormous potential to identify novel QTLs for traits of interest. Due to the availability of cost-effective high-throughput SNP genotyping methods and rapid developments in rice genomics, it is inevitable that these AM approaches will become more popular in the future, especially in the context of genome-wide association studies (GWASs). In this paper, we review the fundamental concepts, critical considerations and limitations of AM focusing on rice, and reiterate the importance of accurate phenotypic data. We also include a section about connecting GWAS to molecular breeding, covering practical consideration for breeders, which is required to use GWAS results in actual rice molecular breeding programs and which has not received adequate attention in the scientific literature.

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Construction of rice chromosome segment substitution lines harboring <i>Oryza barthii</i> genome and evaluation of yield-related traits

Cited by 27 publications

References 36 publications

Accelerating Breeding for Heat Tolerance in Tomato (Solanum lycopersicum L.): An Integrated Approach

Accelerating Breeding for Heat Tolerance in Tomato (Solanum lycopersicum L.): An Integrated Approach

Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

Association mapping in rice: basic concepts and perspectives for molecular breeding

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