QTL Hotspots for Early Vigor and Related Traits under Dry Direct-Seeded System in Rice (Oryza sativa L.)

Abstract

Strong seedling vigor is desirable trait in dry direct-seeded rice (DSR) for enhancing crop establishment and the ability to compete against weeds. A set of 253 BC3F4 lines derived from cross between Swarna and Moroberekan was phenotyped for early vigor (EV) and 8 related traits viz., early uniform emergence (EUE), shoot length (SHL), stem length (SL), shoot fresh weight (SFW), total fresh weight (TFW), shoot dry weight (SDW), total dry weight (TDW), and root dry weight (RDW). Composite interval mapping analysis using genotypic data from 194 SNP markers identified six genomic regions associated with traits on chromosomes 3, 4, 5, and 6 with phenotypic variance ranging from 2.5 to 18.6%. Among them 2 QTL regions; one on chr3 (id3001701-id300833) and the other on chr5 (wd5002636-id5001470) were identified as QTL hotspots A and B respectively and expressed consistently in field as well as glasshouse condition. The majority of QTLs identified for early vigor, and related traits were clustered in the QTL hotspots A (qEV3.1, qEUE3.1, qSHL3.1, qSL3.1, qSFW3.1, qTFW3.1, qRDW3.1) and QTL hotspot B (qEV5.1, qEUE5.1, qSHL5.1, qSL5.1, qSFW5.1, qSDW5.1, qTDW5.1). Ten putative candidate genes viz., 1-alpha-amylase precursor, 2-glutamate decarboxylase, 1-ethylene-insensitive 3, 3-expansin precursor, and 3-phenylalanine ammonia-lyase associated with the target traits were identified in the selected QTL regions. Mutations were identified in the coding region of alpha-amylase precursor and ethylene-insensitive 3 gene between the parents which can be utilized in marker assisted breeding. Trait relationships among the agro-physiological traits were examined to select the best genotypes for the given traits for use in future breeding programs.

Biology of Seed Vigor in the Light of -omics Tools

“…From many seed deterioration experiments, QTLs of seed longevity traits like LD 50 in Arabidopsis seeds [21], germination of aged wheat seeds [48,49] and half-life (P 50 ) of aging barley seeds [50] have been mapped and linked to various genes. For the germination vigor of seeds, several seed priming experiments have found QTLs for germination of maize seeds [51] and QTLs for 30 vigor traits of rice seeds [52] to mention a few. These studies also provided useful information on chromosome regions and putative genes controlling various seed vigor traits in different crops.…”

“…They reported four seed vigor hotspots on chromosome regions for mQTL2, mQTL3-2, mQTL3-4, and mQTL5-2 with large QTL effects under various germination environments. There are a number of recent QTL studies on seed vigor of rice [52,53].…”

“…Singh et al [52] reported seed germination capacity of primed rice seeds derived from 253 BC 3 F 4 lines of crosses between Swarna and Moroberekan, phenotyped for early vigor and genotyped with 194 SNP markers. They identified six seed vigor genomic regions on chromosomes 3, 4, 5, and 6 [52].…”

“…They identified six seed vigor genomic regions on chromosomes 3, 4, 5, and 6 [52]. Two of the QTL regions namely chr3 (id3001701-id300833) and chr5 (wd5002636-id5001470) were identified and tagged QTL hotspots because they were expressed consistently in field and glasshouse conditions.…”

Common genomic regions underlie natural variation in diverse toxin responses

“…Similarly, other QTL hotspots could impact multiple traits, such as responses to various conditions. In yeast, most chemical-response QTL are thought to be unique to one or a few conditions, whereas few QTL have been found to have pleiotropic effects across many conditions (Ehrenreich et al 2012; U. M. Singh et al 2017;Knoch et al 2017). Although QTL underlying responses to individual conditions have been identified across multiple animal models (Najarro et al 2015;Marriage et al 2014;Highfill et al 2017;Bubier et al 2014;Crusio et al 2016), the existence of QTL hotspots that influence multiple condition responses has yet to be observed broadly in metazoans.…”