基于SLAF标记甜瓜果实相关性状和果肉硬度主要候选QTL位点ff2.1的定位

doi:10.1016/j.jia.2023.02.014

摘要/Abstract

摘要：

甜瓜果肉硬度（Flesh firmness, FF）是农业生产者和消费者关注的一个复杂且重要的性状，但目前针对甜瓜果肉硬度性状的遗传机制尚不清楚。本研究以软果肉甜瓜“P5”和硬果肉甜瓜“P10”配置杂交组合，构建F₂分离群体，通过QTL-SLAF测序和分子标记连锁分析，共鉴定112,844个SLAF位点，使用5,919个SNP标记构建了总遗传距离为1356.49 cM的连锁图谱。结合两年田间表型分析显示，控制果实长度（Fruit Length, FL）和宽度（Fruit Diameter, FD）的QTLs位点位于同一区间，控制单果重（Single-Fruit Weight, SFW）性状的QTL位于两条不同的染色体上。对于果肉硬度检测到一个主要QTL位点ff2.1，位于甜瓜2号染色体0.17 Mb的候选区域。利用429个F₂单株，将ff2.1候选区间缩小到28.3 kb区域，包含3个候选基因。本研究不仅鉴定了一个控制甜瓜果肉硬度的QTLs位点，同时也为甜瓜基因功能基因的研究提供了理论基础。

Abstract:

Flesh firmness (FF) is an important and complex trait for melon breeders and consumers. However, the genetic mechanism underlying FF is unclear. Here, a soft fruit melon (P5) and a hard fruit melon (P10) were crossed to generate F₂, and the FF and fruit-related traits were recorded for two years. By performing quantitative trait locus (QTL) specific-locus amplified fragment (SLAF) (QTL-SLAF) sequencing and molecular marker-linkage analysis, 112 844 SLAF markers were identified, and 5 919 SNPs were used to construct a genetic linkage map with a total genetic distance of 1 356.49 cM. Ten FF- and fruit-related QTLs were identified. Consistent QTLs were detected for fruit length (FL) and fruit diameter (FD) in both years, and QTLs for single fruit weight (SFW) were detected on two separate chromosomes in both years. For FF, the consistent major locus (ff2.1) was located in a 0.17-Mb candidate region on chromosome 2. Using 429 F₂ individuals derived from a cross between P5 and P10, we refined the ff2.1 locus to a 28.3-kb region harboring three functional genes. These results provide not only a new candidate QTL for melon FF breeding but also a theoretical foundation for research on the mechanism underlying melon gene function.

Key words: QTL mapping , flesh firmness , fruit-related traits , melon , and SLAF sequencing

. 基于SLAF标记甜瓜果实相关性状和果肉硬度主要候选QTL位点ff2.1的定位[J]. Journal of Integrative Agriculture, 2023, 22(11): 3331-3345.

CHEN Ke-xin, DAI Dong-yang, WANG Ling, YANG Li-min, LI Dan-dan, WANG Chao, JI Peng, SHENG Yun-yan. SLAF marker based QTL mapping of fruit-related traits reveals a major-effect candidate locus ff2.1 for flesh firmness in melon[J]. Journal of Integrative Agriculture, 2023, 22(11): 3331-3345.

参考文献

Amanullah S, Liu S, Gao P, Zhu Z C, Zhu Q L, Fan C, Luan F S. 2018. QTL mapping for melon (Cucumis melo L.) fruit traits by assembling and utilization of novel SNPs based CAPS markers. Scientia Horticulturae, 236, 18–29.

Ayub R, Guis M, Ben Amor M, Gillot L, Roustan J P, Latché A, Bouzayen M, Pech J C. 1996. Expression of ACC oxidase antisense gene inhibits ripening of cantaloupe melon fruits. Nature Biotechnology, 14, 862–866.

Bhat J A, Ali S, Salgotra R K, Mir Z A, Dutta S, Jadon V, Tyagi A, Mushtaq M, Jain N, Singh P K, Singh G P, Prabhu K V. 2016. Genomic selection in the era of next generation sequencing for complex traits in plant breeding. Frontiers in Genetics, 7, 221.

Castanera R, Ruggieri V, Pujol M, Garcia-Mas J, Casacuberta J M. 2020. An improved melon reference genome with single-molecule sequencing uncovers a recent burst of transposable elements with potential impact on genes. Frontiers in Plant Science, 10, 1815.

Chaïb J, Devaux M F, Grotte M G, Robini K, Causse M, Lahaye M, Marty I. 2007. Physiological relationships among physical, sensory, and morphological attributes of texture in tomato fruits. Journal of Experimental Botany, 58, 1915–1925.

Chao Y U, Wan H H, Bourke P M, Cheng B X, Zhang Q X. 2021. High density genetic map and quantitative trait loci (QTLs) associated with petal number and flower diameter identified in tetraploid rose. Journal of Integrative Agriculture, 20, 1287–1301.

Chapman N H, Bonnet J, Grivet L, Lynn J, Graham N, Smith R, Sun G, Walley P G, Poole M, Causse M, King G J, Baxter C, Seymour G B. 2012. High resolution mapping of a fruit firmness-related QTL in tomato reveals epistatic interactions associated with a complex combinatorial locus. Plant Physiology, 159, 1644–1657.

Cuevas H E, Staub J E, Simon P W, Zalapa J E. 2009. A consensus linkage map identifies genomic regions controlling fruit maturity and beta-carotene-associated flesh color in melon (Cucumis melo L.). Theoretical and Applied Genetics, 119, 741–756.

Cuevas H E, Staub J E, Simon P W, Zalapa J E, McCreight J D. 2008. Mapping of genetic loci that regulate quantity of beta-carotene in fruit of US Western Shipping melon (Cucumis melo L.). Theoretical and Applied Genetics, 117, 1345–1359.

Dai D Y, Zeng S, Wang L, Li J F, Ji p, Liu H Y, Sheng Y Y. 2022. Identification of fruit firmness QTL ff2.1 by SLAF-BSA and QTL mapping in melon. Euphytica, 218, 52 .

Díaz A, Martín-Hernández A M, Dolcet-Sanjuan R, Garcés-Claver A, Álvarez J M, Garcia-Mas J, Picó B, Monforte A J. 2017. Quantitative trait loci analysis of melon (Cucumis melo L.) domestication-related traits. Theoretical and Applied Genetics, 130, 1837–1856.

Díaz A, Zarouri B, Fergany M, Eduardo I, Alvarez J M, Picó B, Monforte A J. 2014. Mapping and introgression of QTL involved in fruit shape transgressive segregation into ‘Piel de Sapo’ melon (Cucumis melo L.). PLoS ONE, 9, e104188.

Farcuh M, Copes B, Le-Navenec G, Marroquin J, Jaunet T, Chi-Ham C, Van Deynze A. 2020. Texture diversity in melon (Cucumis melo L.): Sensory and physical assessments. Postharvest Biology and Technology, 159, 111024.

Frary A, Doganlar S, Frampton A, Fulton T, Uhlig J, Yates H, Tanksley S. 2003. Fine mapping of quantitative trait loci for improved fruit characteristics from Lycopersicon chmielewskii chromosome 1. Genome, 46, 235–243.

Fukino N, Ohara T, Monforte A J, Sugiyama M, Sakata Y, Kunihisa M, Matsumoto S. 2008. Identification of QTLs for resistance to powdery mildew and SSR markers diagnostic for powdery mildew resistance genes in melon (Cucumis melo L.). Theoretical and Applied Genetics, 118, 165–175.

Galpaz N, Gonda I, Shem-Tov D, Barad O, Tzuri G, Lev S, Fei Z, Xu Y, Mao L, Jiao C, Harel-Beja R, Doron-Faigenboim A, Tzfadia O, Bar E, Meir A, Sa’ar U, Fait A, Halperin E, Kenigswald M, Fallik E, et al. 2018. Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based high-resolution QTL and eQTL mapping. Plant Journal, 94, 169–191.

Gao Y, Guo Y, Su Z, Yu Y, Zhu Z, Gao P, Wang X. 2020. Transcriptome analysis of genes related to fruit texture in watermelon. Scientia Horticulturae, 262, 109075.

Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González V M, Puigdomènech P. 2012. The genome of melon (Cucumis melo L.). Proceedings of the National Academy of Sciences of the United States of America, 109, 11872–11877.

Giménez E, Dominguez E, Pineda B, Heredia A, Moreno V, Lozano R, Angosto T. 2015. Transcriptional activity of the MADS box ARLEQUIN/TOMATO AGAMOUS-LIKE1 gene is required for cuticle development of tomato fruit. Plant Physiology, 168, 1036–1048.

Goulao L F, Oliveira C M. 2008. Cell wall modifications during fruit ripening: When a fruit is not the fruit. Trends in Food Science & Technology, 19, 4–25.

Guo S, Sun H, Zhang H, Liu J, Ren Y, Gong G, Jiao C, Zheng Y, Yang W, Fei Z, Xu Y. 2015. Comparative transcriptome analysis of cultivated and wild watermelon during fruit development. PLoS ONE, 10, e0130267.

Harel-Beja R, Tzuri G, Portnoy V, Lotan-Pompan M, Lev S, Cohen S, Dai N, Yeselson L, Meir A, Libhaber S E, Avisar E, Melame T, van Koert P, Verbakel H, Hofstede R, Volpin H, Oliver M, Fougedoire A, Stalh C, Fauve J, et al. 2010. A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes. Theoretical and Applied Genetics, 121, 511–533.

Hu Z, Deng G, Mou H, Xu Y, Chen L, Yang J, Zhang M. 2018. A re-sequencing-based ultra-dense genetic map reveals a gummy stem blight resistance-associated gene in Cucumis melo. DNA Research, 25, 1–10.

Jiang B, Liu W, Xie D, Peng Q, He X, Lin Y, Liang Z. 2015. High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing. BMC Genomics, 16, 1035.

Kesh H, Kaushik P. 2021. Advances in melon (Cucumis melo L.) breeding: An update. Scientia Horticulturae, 282, 110045.

Li R, Sun S, Wang H, Wang K, Yu H, Zhou Z, Xin P, Chu J, Zhao T, Wang H, Li J, Cui X. 2020. FIS1 encodes a GA2-oxidase that regulates fruit firmness in tomato. Nature Communications, 11, 5844.

Lian Q, Fu Q, Xu Y, Hu Z, Zheng J, Zhang A, He Y, Wang C, Xu C, Chen B, Garcia-Mas J, Zhao G, Wang H. 2021. QTLs and candidate genes analyses for fruit size under domestication and differentiation in melon (Cucumis melo L.) based on high resolution maps. BMC Plant Biology, 21, 126.

Liu L, Sun T, Liu X, Guo Y, Huang X, Gao P, Wang X. 2019. Genetic analysis and mapping of a striped rind gene (st3) in melon (Cucumis melo L.). Euphytica, 215, 1–12.

Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25, 402–408.

Luan F S, Sheng Y Y, Wang Y, Staub J E. 2010. Performance of melon hybrids derived from parents of diverse geographic origins. Euphytica, 173, 1–16.

Monforte A J, Oliver M, Gonzalo M J, Alvarez J M, Dolcet-Sanjuan R, Arffls P. 2004. Identification of quantitative trait loci involved in fruit quality traits in melon (Cucumis melo L.). Theoretical and Applied Genetics, 108, 750–758.

Moreno E, Obando J M, Dos-Santos N, Fernández-Trujillo J P, Monforte A J, Garcia-Mas J. 2008. Candidate genes and QTLs for fruit ripening and softening in melon. Theoretical and Applied Genetics, 116, 589–602.

Murakami M, Kudo I. 2002. Phospholipase A2. Biochemical Journal, 131, 285–292.

Nimmakayala P, Tomason Y R, Abburi V L, Alvarado A, Saminathan T, Vajja V G, Salazar G, Panicker G K, Levi A, Wechter W P, McCreight J D, Korol A B, Ronin Y, Garcia-Mas J, Reddy U K. 2016. Genome-wide differentiation of various melon horticultural groups for use in GWAS for fruit firmness and construction of a high resolution genetic map. Frontiers in Plant Science, 7, 1437.

Pan Y P, Wang Y H, McGregor C, Liu S, Luan F S, Gao M L, Weng Y Q. 2020. Genetic architecture of fruit size and shape variation in cucurbits: A comparative perspective. Theoretical and Applied Genetics, 133, 1–21.

Pereira L, Ruggieri V, Pérez S, Alexiou K G, Fernández M, Jahrmann T, Pujol M, Garcia-Mas J. 2018. QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map. BMC Plant Biology, 18, 324.

Pereira L, Santo Domingo M, Argyris J, Mayobre C, Valverde L, Martín-Hernández A M, Pujol M, Garcia-Mas J. 2021. A novel introgression line collection to unravel the genetics of climacteric ripening and fruit quality in melon. Scientific Reports, 11, 11364.

Pereira L, Santo Domingo M, Ruggieri V, Argyris J, Phillips M A, Zhao G, Lian Q, Xu Y, He Y, Huang S, Pujol M, Garcia-Mas J. 2020. Genetic dissection of climacteric fruit ripening in a melon population segregating for ripening behavior. Horticulture Research, 7, 187.

Perpiñá G, Esteras C, Gibon Y, Monforte A J, Picó B. 2016. A new genomic library of melon introgression lines in a cantaloupe genetic background for dissecting desirable agronomical traits. BMC Plant Biology, 16, 154.

Qi Z, Huang L, Zhu R, Xin D, Liu C, Han X, Jiang H, Hong W, Hu G, Zheng H, Chen Q. 2014. A high-density genetic map for soybean based on specific length amplified fragment sequencing. PLoS ONE, 9, e104871.

Romero P, Gandía M, Alférez F. 2013. Interplay between ABA and phospholipases A(2) and D in the response of citrus fruit to postharvest dehydration. Plant Physiology and Biochemistry, 70, 287–294.

Sahu P K, Sao R, Mondal S, Vishwakarma G, Gupta S K, Kumar V, Singh S, Sharma D, Das B K. 2020. Next generation sequencing based forward genetic approaches for identification and mapping of causal mutations in crop plants: A comprehensive review. Plants, 9, 1355.

Sun L, Zhang Y, Cui H, Zhang L, Sha T, Wang C, Fan C, Luan F, Wang X. 2020. Linkage mapping and comparative transcriptome analysis of firmness in watermelon (Citrullus lanatus). Frontiers in Plant Science, 11, 831.

Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, Jiang C, Guan N, Ma C, Zeng H, Xu C, Song J, Huang L, Wang C, Shi J, Wang R, Zheng X, Lu C, Wang X, Zheng H. 2013. SLAF-seq: An efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS ONE, 8, e58700.

Tanksley S D, Grandillo S, Fulton T M, Zamir D, Eshed Y, Petiard V, Lopez J, Beck-Bunn T. 1996. Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theoretical and Applied Genetics, 92, 213–224.

Toivonen P M. 2008. Influence of harvest maturity on cut-edge browning of ‘Granny Smith’ fresh apple slices treated with anti-browning solution after cutting. LWT-Food Science and Technology, 41, 1607–1609.

Uluisik S, Chapman N H, Smith R, Poole M, Adams G, Gillis R B, Besong T M, Sheldon J, Stiegelmeyer S, Perez L, Samsulrizal N, Wang D, Fisk I D, Yang N, Baxter C, Rickett D, Fray R, Blanco-Ulate B, Powell A L, Harding S E, et al. 2016. Genetic improvement of tomato by targeted control of fruit softening. Nature Biotechnology, 34, 950–952.

Vegas J, Garcia-Mas J, Monforte A J. 2013. Interaction between QTLs induces an advance in ethylene biosynthesis during melon fruit ripening. Theoretical and Applied Genetics, 126, 1531–1544.

Wang J, Su K, Guo Y, Xing H, Zhao Y, Liu Z, Li K, Guo X. 2017. Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing. PLoS ONE, 12, e0181728.

Wang Y H, Wu D H, Huang J H, Tsao S J, Hwu K K, Lo H F. 2016. Mapping quantitative trait loci for fruit traits and powdery mildew resistance in melon (Cucumis melo). Botanical Studies, 57, 19.

Wen Y, Zhang S, Wang J, He J, Cai D, Zhao L, Wang D. 2018. Fine mapping of lobed-leaf genes in two Brassica napus lines using SLAF sequencing. Crop Science, 58, 1684–1692.

Xu X, Ji J, Xu Q, Qi X, Weng Y, Chen X. 2018. The major effect quantitative trait locus CsARN6.1 encodes an AAA ATPase domain containing protein that is associated with waterlogging stress tolerance by promoting adventitious root formation. Plant Journal, 93, 917–930.

Yang T, Amanullah S, Pan J, Chen G, Liu S, Ma S, Wang X. 2021. Identification of putative genetic regions for watermelon rind hardness and related traits by BSA-seq and QTL mapping. Euphytica, 217, 1–18.

Yi L, Wang Y, Huang X, Gong Y, Wang S, Dai Z. 2020. Genome-wide identification of flowering time genes in cucurbit plants and revealed a gene ClGA2/KS associate with adaption and flowering of watermelon. Molecular Biology Reports, 47, 1057–1065.

Zalapa J E, Staub J E, McCreight J D, Chung S M, Cuevas H. 2007. Detection of QTL for yield-related traits using recombinant inbred lines derived from exotic and elite US Western shipping melon germplasm. Theoretical and Applied Genetics, 114, 1185–1201.

Zarid M, García-Carpintero V, Esteras C, Esteva J, Bueso M C, Cañizares J, Picó M B, Monforte A. J, Fernández-Trujillo J P. 2021. Transcriptomic analysis of a near-isogenic line of melon with high fruit flesh firmness during ripening. Journal of the Science of Food and Agriculture, 101, 754–777.

Zhang Y, Wang L, Xin H, Li D, Ma C, Ding X, Hong W, Zhang X. 2013. Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing. BMC Plant Biology, 13, 141.

Zheng Y, Xu F, Li Q, Wang G, Liu N, Gong Y, Li L, Chen Z H, Xu S. 2018. QTL mapping combined with bulked segregant analysis identify SNP markers linked to leaf shape traits in Pisum sativum using SLAF sequencing. Frontiers in Genetics, 9, 615.

Zhu W Y, Huang L, Chen L, Yang J T, Wu J N, Qu M L, Yao D Q, Guo C L, Lian H L, He H L, Pan J S, Cai R. 2016. A high-density genetic linkage map for cucumber (Cucumis sativus L.): Based on specific length amplified fragment (SLAF) sequencing and QTL analysis of fruit traits in cucumber. Frontiers in Plant Science, 7, 437.