Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations

Abstract

Spike density (SD) is an agronomically important character in wheat. In addition, an optimized spike structure is a key basis for high yields. Identification of quantitative trait loci (QTL) for SD has provided a genetic basis for constructing ideal spike morphologies in wheat. In this study, two recombinant inbred line (RIL) populations (tetraploid RIL AM and hexaploid RIL 20828/SY95-71 (2SY)) previously genotyped using the wheat55K SNP array were used to identify SD QTL. A total of 18 QTL were detected, and three were major and one was stably expressed (QSd.sau-2SY-7A.2, QSd.sau-AM-5A.2, QSd.sau-AM-7B, and QSd.sau-2SY-2D). They can explain up to 23.14, 19.97, 12.00, and 9.44% of phenotypic variation, respectively. QTL × environment and epistatic interactions for SD were further analyzed. In addition, pyramiding analysis further revealed that there were additive effects between QSd.sau-2SY-2D and QSd.sau-2SY-7A.2 in 2SY, and QSd.sau-AM-5A.2 and QSd.sau-AM-7B in AM. Pearson’s correlation between SD and other agronomic traits, and effects of major or stable QTL on yield related traits indicated SD significantly impacted spike length (SL), spikelet number per spike (SNS) and kernel length (KL). Several genes related to spike development within the physical intervals of major or stable QTL were predicted and discussed. Collectively, our research identified QTL with potential applications for modern wheat breeding and broadening the genetic basis of SD.

Genetic Dissection of Three Major Quantitative Trait Loci for Spike Compactness and Length in Bread Wheat (Triticum aestivum L.)

“…For instance, QSD.SAU-2N.2 and QSc.cau-2D.1 for SC were located in the interval of 405.73–654.34 and 423.69–654.34 Mb, which were much larger than QSc/Sl.cib-2D ( Gao et al, 2016b ; Zhai et al, 2016 ). Qsd.sac-2D , QSd.sau-2SY-2D , QSd.sicau-2D.3 and the marker IWB26541 for SC reported previously located within 588.68–612.82, 602.76–610.04, 605.12–609.88 and 611.14 Mb were overlapped and covered the interval in the present study ( Luo et al, 2016 ; Liu et al, 2018 , 2019 ; You et al, 2021 ). Among them, QTL for SL and SNS were detected at the locus QSc.cau-2D.1 in the interval of 423.69–654.34 Mb, indicating that it was a multiple effect locus ( Zhai et al, 2016 ).…”

“…Among them, QTL for SL and SNS were detected at the locus QSc.cau-2D.1 in the interval of 423.69–654.34 Mb, indicating that it was a multiple effect locus ( Zhai et al, 2016 ). In addition, previous studies revealed that QSd.sau-2SY-2D exerted pleiotropic effects on SL, SNS and TKW ( You et al, 2021 ). Moreover, QSc/Sl.cib-2D had pleiotropic effects on PHT, GLW, GL and GR ( Figure 7 ).…”

“…Integrating multiple favorable alleles into a genetic background was considered to be an effective strategy to optimize traits for yield increasing in wheat ( Fan et al, 2019 ; Li et al, 2021a , b ; Tu et al, 2021 ; You et al, 2021 ). QSc/Sl.cib-2AS or QSc/Sl.cib-2AL alone had no significant effect on SC and SL, but QSc/Sl.cib-2D alone could strongly decrease SL by 12.76% and increase SC by 12.45%, respectively ( Figure 6 ).…”

“…The spike is the reproductive organ of the wheat plant and is an essential component to produce and hold grains ( Faris et al, 2014 ). The morphological traits of a spike, including spike compactness (SC), spike length (SL), and spikelet number per spike (SNS), have been found to be greatly associated with grain yield in previous studies ( Chai et al, 2019 ; Wolde et al, 2019 ; Li et al, 2021a ; You et al, 2021 ). Therefore, the identification of major and stable quantitative trait loci (QTL)/genes for SC and SL is an efficient strategy to cultivate and domesticate high-yield varieties with the ideal plant architecture in wheat for breeders ( Ma et al, 2007 ; Faris et al, 2014 ).…”

Identification and validation of a locus for wheat maximum root length independent of parental reproductive environment

“…The inclusive composite interval mapping-additive and dominance of biparental population module (BIP) in IciMapping v4.2 ( Meng et al, 2015 ) was used to detect QTL for MRL. The running speed, PIN value, and logarithm of odds (LOD) value of threshold were set at 1.0 cM, 0.001, 3, respectively ( You et al, 2021 ). QTL identified in more than two tests were considered to be stably expressed.…”