TIP41L, a putative candidate gene conferring both seed size and boll weight, was fine-mapped in an introgression line of Gossypium hirsutum-Gossypium arboreum

Feng, Liuchun; Su, Qiao; Yue, Haoran; Wang, Liang; Gao, Jianbo; Xing, Liangshuai; Xu, Min; Zhou, Chenhui; Yang, Ying; Zhou, Baoliang

doi:10.1016/j.plantsci.2022.111197

Cited by 2 publications

(3 citation statements)

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“…Many candidate genes of the QTLs for LP and BW have been studied [ 48 – 50 , 55 ]. The TIP41-like family protein ( TIP41L ) gene ( GH_A12G0194 ) is thought to be the candidate gene of a stable major QTL ( q ( BW + SI ) -A12-1 ) for BW [ 49 ]. One gene orthologous to the Arabidopsis receptor-like protein kinase gene HERK1 ( GB_A07G1034 ) was predicted to be the candidate gene for LP in G. barbadense [ 48 ].…”

Section: Discussionmentioning

confidence: 99%

“…Although the inheritance, QTLs and candidate genes of LP and BW in upland cotton have been widely studied, only a few of the studied QTLs have been used in the molecular breeding of cotton via marker-assisted selection (MAS) [ 49 , 50 ]. One of the reasons is that the identified QTLs are unstable in multiple-environments and only explain little phenotypic variance.…”

Section: Introductionmentioning

confidence: 99%

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Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60

et al. 2023

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Background Upland cotton (Gossypium hirsutum L.) is the most economically important species in the cotton genus (Gossypium spp.). Enhancing the cotton yield is a major goal in cotton breeding programs. Lint percentage (LP) and boll weight (BW) are the two most important components of cotton lint yield. The identification of stable and effective quantitative trait loci (QTLs) will aid the molecular breeding of cotton cultivars with high yield. Results Genotyping by target sequencing (GBTS) and genome-wide association study (GWAS) with 3VmrMLM were used to identify LP and BW related QTLs from two recombinant inbred line (RIL) populations derived from high lint yield and fiber quality lines (ZR014121, CCRI60 and EZ60). The average call rate of a single locus was 94.35%, and the average call rate of an individual was 92.10% in GBTS. A total of 100 QTLs were identified; 22 of them were overlapping with the reported QTLs, and 78 were novel QTLs. Of the 100 QTLs, 51 QTLs were for LP, and they explained 0.29–9.96% of the phenotypic variation; 49 QTLs were for BW, and they explained 0.41–6.31% of the phenotypic variation. One QTL (qBW-E-A10-1, qBW-C-A10-1) was identified in both populations. Six key QTLs were identified in multiple-environments; three were for LP, and three were for BW. A total of 108 candidate genes were identified in the regions of the six key QTLs. Several candidate genes were positively related to the developments of LP and BW, such as genes involved in gene transcription, protein synthesis, calcium signaling, carbon metabolism, and biosynthesis of secondary metabolites. Seven major candidate genes were predicted to form a co-expression network. Six significantly highly expressed candidate genes of the six QTLs after anthesis were the key genes regulating LP and BW and affecting cotton yield formation. Conclusions A total of 100 stable QTLs for LP and BW in upland cotton were identified in this study; these QTLs could be used in cotton molecular breeding programs. Putative candidate genes of the six key QTLs were identified; this result provided clues for future studies on the mechanisms of LP and BW developments.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60

et al. 2023

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“…Many candidate genes have been identi ed through QTL mapping and map-based cloning. For example, GbCML7 was suggested to regulate boll number (BN) in some backgrounds [38], TIP41L [39] and GhDA1-1A [40] were speculated to be the putative candidate genes responsible for both cotton seed size and boll weight, while Gh_D01G0162, Gh_D07G0465 [41], and GB_A07G1034 [42] were identi ed as candidate LP-determining genes. For ber quality, Ghir_A10G022020 was proposed to act as a negative regulator of FL by interacting with NF-YA [43], whereas GB_D11G3437, GB_D11G3460, and GB_D11G3471 were found to be associated with FS [42].…”

Section: Introductionmentioning

confidence: 99%

Quantitative trait loci mapping and candidate gene analysis for cotton yield, fiber quality, and early maturity

Jia,

Zhao,

Zhu

et al. 2024

Preprint

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Background Cotton is the most important natural fiber-producing crop globally. High yield, super quality fiber, and early maturity are equally important breeding goals in the cotton industry. However, it remains challenging to synchronously improve these traits through conventional breeding techniques.Methods To identify additional genetic information relating to yield, fiber quality, and early maturity, a high-density genetic map was constructed using Jifeng 1271 and Jifeng 173 cultivars as parents. Sixteen phenotypic traits were tested and quantitative trait locus (QTL) mapping was performed. Candidate genes were analyzed using published RNA-seq data and qRT-PCR assays.Results All 16 tested traits showed bi-directional transgressive segregation and most traits followed an approximately normal distribution. Overall, 33 and 12 trait pairs showed significant positive and significant negative correlations, respectively. A total of 317 QTL and 39 chromosomal regions containing overlapping QTL were mapped based on the generated high-density genetic map, including 18 stable and 18 major QTL. Three outstanding QTL—qLP-A13-3, qSI-A2-1, and qFL-D13-1—that could be repeatedly mapped and had a major additive effect on phenotypic variation were screened out. Thirteen trait pairs exhibiting significant positive correlations contained overlapping QTL, and overlapping QTL within the same region exhibited the same additive-effect directions. Ten trait pairs showing significant negative correlations also had overlapping QTL; for 8 of these pairs, the QTL within a region had opposite additive-effect directions. Four genes locating in the mapped QTL regions were screened out due to their high expression levels in the evaluated RNA-seq datasets and their annotated functions. Ghir_A04G014830.1, covered by qBW-A4-1, qSI-A401, qHNFFB-A4-1, and qFU-A4-1, encoded ACLA-1. Ghir_D07G023700.1, covered by qFT-D7-1, qNFFB-D7-1, qHNFFB-D7-1, qFU-D7-1, qFE-D7-1, and qFE-D7-2, encoded ALDH2B4. Ghir_D13G015010.1, encoding VTC2, and Ghir_D13G016670.1, encoding GA2OX1, were in the stable QTL qFL-D13-1 region. The qRT-PCR results relating to the expression patterns of these four genes in ovules and fibers suggested that these four genes may be involved in promoting seed development, fiber initiation, and fiber elongation.Conclusions Overall, these findings contribute additional information for the breeding of high-yield, super fiber quality, and early-maturity varieties as well as research on related molecular mechanisms.

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TIP41L, a putative candidate gene conferring both seed size and boll weight, was fine-mapped in an introgression line of Gossypium hirsutum-Gossypium arboreum

Cited by 2 publications

References 63 publications

Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60

Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60

Quantitative trait loci mapping and candidate gene analysis for cotton yield, fiber quality, and early maturity

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