Euphytica

Hu, Yanling; Huang, Xuhui; Wang, Fang; He, Yu; Feng, Lihua; Jiang, Bo; Hao, Ming; Ning, Shunzong; Yuan, Zhongwei; Wu, Jiajie; Zhang, Lianquan; Wu, Bihua; Liu, Dengcai; Huang, Lin

doi: 10.1007/s10681-021-02937-2pmid: N/A

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a destructive fungal disease with a significant economic impact. Aegilops tauschii, the D-genome progenitor of wheat (Triticum aestivum, AABBDD), offers valuable gene pool for Pst resistance. The Ae. tauschii gene YrAS2388 confers resistance to a wide range of Pst races and encodes a typical nucleotide oligomerization domain-like receptor (NLR). The functional YrAS2388R has duplicated 3′ untranslated regions (3′UTRs). In the present study, we have developed two gene-specific kompetitive allele specific PCR (KASP) markers for YrAS2388R by comparing multiple homoeologous and paralogous genomic sequences of YrAS2388 alleles from allopolyploid wheat genomes. KASP-E5 was developed based on SNP in the exon5 sequences of YrAS2388, which behaves as a co-dominant marker. KASP-E6′ was developed based on the 3′UTR sequences of YrAS2388, which behaves as a dominant marker. These markers were validated in different types of wheat populations and showed clear functional differentiation that was completely agreement with the gel based gene-specific marker for YrAS2388R. Our results indicate that KASP-E5 and KASP-E6′ are perfect diagnostic markers for YrAS2388R and would be useful for marker assisted selection in wheat resistance breeding.

Liu, Yanmei; Zhang, Lu; Sun, Yanni; Zhou, Shujun

doi: 10.1007/s10681-021-02935-4pmid: N/A

It has been reported that F1 LA hybrids could produce a small number of functional 2n eggs regardless of their male sterility, however, there are very little similar phenomena reported in OA, LO, or OT hybrids, though there are many allotriploid cultivars in flower markets, involving distant hybrids. To investigate the occurrence of 2n eggs in distant lily F1 hybrids, a diploid OT hybrid was analyzed for its meiosis and progenies using conventional method and genomic in situ hybridization. The results showed that the diploid OT hybrid had abnormal meiosis and was highly male sterile, however, as seed parent, its progenies were triploid or near triploid, implying that it could produce a small number of functional 2n eggs. The genome compositions of the triploids indicated that the functional 2n eggs were predominantly from first division restitution mechanism, though they were variable due to the differences among their intergenomic recombinant chromosomes. In addition, all the progenies grew vigorously and variously, especially for their flower color, demonstrating that the polyploidization and variable intergenomic recombinations were important for breeding lily cultivars from BC1 progenies. It is concluded, in Lilium breeding, that the occurrence of a small number of functional 2n eggs in F1 distant hybrids is quite common, and their triploid progenies are the main origin of allotriploid lily cultivars.

Abady, Seltene; Shimelis, Hussein; Janila, Pasupuleti; Deshmukh, Dnyaneshwar; Wankhade, Ankush; Chaudhari, Sunil; Manohar, Surendra S.

doi: 10.1007/s10681-021-02932-7pmid: N/A

Genetic advancement and gains in yield and related traits are dependent on the selection of best combiner parents and progenies under the prevailing growing conditions. This study was conducted to determine the combining ability effects of eight selected drought-tolerant groundnut parental lines and their F2 progenies under drought-stressed (DS) and non-stressed (NS) conditions to determine the gene actions involved in the inheritance of the studied traits and identify the best parents and progenies for further improvement of the crop for moisture stress tolerance. Experiments were conducted at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in India during 2020 cropping season. Data on some of the important physiological, yield and yield component traits were collected. The general combining ability (GCA) effects of parents were significant (P < 0.05) for all assessed traits under all testing conditions, except for PB under DS and NS conditions in the glasshouse. The specific combining ability (SCA) effects of progenies were significant (P < 0.05) for all traits, except for PH across all testing environments and PB under field conditions. The genotype ICGV 10178 was the best general combiner with positive contribution and significance to SCMR, PY, SHP, KY, TBM and HI and reduced SLA. Crosses ICGV 10178 × ICGV 11369, ICGV 10373 × ICGV 15083, ICGV 98412 × ICGV 15094 and ICGV 10178 × ICGV 98412 were the best specific combiners for enhanced pod yield and drought tolerance. The GCA was found predominant over the SCA effect for the inheritance of PY, KY and TBM. Higher GCA: SCA rations were recorded for PY and KY under both DS and NS conditions, and SCMR, SLA and TBM under DS condition suggesting the predominant role of additive genes conditioning the inheritance of these traits. Therefore, the above new progenies are useful populations for developing improved pure line groundnut varieties with high pod yield and drought tolerance.

Alemu, Admas; Suliman, Sufian; Hagras, Adel; Thabet, Sherif; Al-Abdallat, Ayed; Abdelmula, Awadalla Abdalla; Tadesse, Wuletaw

doi: 10.1007/s10681-021-02933-6pmid: N/A

Identification and exploration of the genetic architecture of traits related to yield, quality, and drought and heat tolerance is important for yield and quality improvement of wheat through marker-assisted selection. One hundred and ninety-two spring wheat genotypes were tested at two heat-stress locations in Sudan (Wad Medani and Dongula), a drought stress site in Morocco (Marchouch) and a site with high yield potential in Egypt (Sids) in replicated trials during the 2015–2016 and 2016–2017 cropping seasons. A total of 10,577 single nucleotide polymorphism markers identified from the 15 K wheat SNP assay were used in a genome-wide association (GWA) study and genomic prediction for 16 phenotypic traits related to yield, quality and drought and heat tolerance. Significant marker-trait associations were detected across GWAS models for all traits. Most detected marker-trait associations (MTAs) were environment-specific, signifying the presence of high quantitative trait loci-by-environment (QTL x E) interaction. Chromosome arm 5AL had significant multi-model MTAs for grain yield and yield-related traits at the heat-stress locations. Highly significant QTLs were detected on chromosome 2D for waxiness. Homoeologous group 2 and 6 chromosomes were with significant MTAs for grain protein content, gluten content, alveograph strength and Zeleny sedimentation test while chromosome arm 3BL was significant for both Z and W traits. Genomic prediction analysis with ridge regression-best linear unbiased prediction model estimated the breeding values of the studied traits with prediction accuracies ranging from 0.16 for leaf rolling to 0.72 for peduncle length. The identified QTLs could be targeted for marker-assisted selection or further studies aimed at fine mapping and cloning the causative genes and detecting favorable haplotypes with positive effects for agronomic, physiological or quality-related traits.

He, Qingyuan; Xiang, Shihua; Yang, Huawei; Wang, Wubin; Shu, Yingjie; Li, Zhengpeng; Yang, Xiaoyan; Wang, Songhua

doi: 10.1007/s10681-021-02931-8pmid: N/A

Soybean seeds contain high levels of oil and protein, providing 57 and 69% of a person's dietary requirements, respectively. Although many quantitative trait loci for the 100-seed weight (100SW), protein content (PRC), and oil content (OIC) have been reported, their genetic controls in soybeans remain unclear. The QTL–allele constitution of three traits in the Sichuan and Chongqing eco-regions population (SCLBP) was studied using a representative sample composed of 228 accessions. These were tested in four environments and analyzed using 135 simple sequence repeats (SSR) and 107,081 valid single nucleotide polymorphism linkage (SNP) markers. The range of 100SW, PRC, and OIC in SCLBP accessions were 4.82–33.35, 36.47–49.75%, and 14.68–21.77%, respectively. The heritability (h2) and genetic coefficient of variation (GCV) of the three traits were high. As a result, 26, 33, and 31 QTLs were found using SSR for 100SW, PRC, and OIC, respectively. The allele of Sat_260 for 100SW was detected in the four environments. In addition, 28, 198, and 250 loci for 100SW, PRC, and OIC, respectively, were found using SNP and mixed linear model (MLM). Further SNP haplotype analysis revealed that 13, 35, and 60 blocks were found for 100SW, RPC, and OIC, respectively. The block of Gm11_9895764-9,917,646 for 100SW was simultaneously detected in the four environments. Among these QTLs, 1, 5, and 7 for 100SW, PRC and OIC were found using two methods of SSR and SNP at the same time. A majority of these QTLs overlapped with the previously reported loci. However, 9, 11, and 9 loci for 100SW, PRC, and OIC using SSR; and 3, 5, and 8 for 100SW, PRC, and OIC hadn’t been reported using SNP. Moreover, the genes of Glyma.11g130800, Glyma.13g217000, and Glyma.08g122600 were considered the most likely genes controlling 100SW, PRC, and OIC, respectively. These findings provide evidence for mixed major plus polygenes inheritance for the three traits and an extended understanding of their genetic architecture for the molecular dissection and breeding of soybeans.

Samantara, Kajal; Reyes, Vincent P.; Agrawal, Nisha; Mohapatra, Sourav Ranjan; Jena, Kshirod K.

doi: 10.1007/s10681-021-02934-5pmid: N/A

Ravelombola, Waltram; Manley, Aurora; Adams, Curtis; Trostle, Calvin; Ale, Srinivasulu; Shi, Ainong; Cason, John

doi: 10.1007/s10681-021-02929-2pmid: N/A

Guar, [Cyamopsis tetragonoloba (L.) Taub] is an annual summer legume that is widely grown in arid and semi-arid regions. It is a diploid legume (2n = 2x = 14) with a genome size of approximately 560 Mb. Guar can fix atmospheric nitrogen via a symbiotic process with rhizobial bacteria, thus enhancing soil fertility and decreasing the need for the use of expensive nitrogen (N) fertilizers. Guar is a drought- and heat-tolerant crop and can be grown using minimal agricultural inputs. Guar can be used as vegetable, feed/fodder, or green manure. One of the primary driving factors for guar cultivation is galactomannan gum, known as guar gum, found in the seed endosperm. Guar gum has various industrial uses that range from cosmetic applications, food ingredients, to the oil industries. India is the lead guar production and accounts for more than 80% of the world production. The U.S. is the world largest guar market. This review discusses the status of genomic resources in guar, the progress made for germplasm evaluation of various agronomic traits, and the genetic engineering efforts in guar.

Gaudin, Amanda G.; Wubben, Martin J.

doi: 10.1007/s10681-021-02938-1pmid: N/A

The root-knot nematode (RKN; Meloidogyne incognita) and reniform nematode (RN; Rotylenchulus reniformis) reduce Upland cotton (Gossypium hirsutum) yields nearly 5% annually throughout the United States. Recent work has proved successful in transferring the chromosome 11 (Chr11) and 14 RKN resistance QTL and the chromosome 21 Renbarb2 RN resistance QTL into elite Upland cultivars. The deployment of a limited number of resistance QTL risks the creation of virulent nematode populations; therefore, we set out to phenotypically and genotypically re-evaluate wild G. hirsutum and G. barbadense accessions that had previously been labeled as resistant to RKN and/or RN. Twenty-six (26) G. hirsutum accessions were evaluated for RKN resistance and were genotyped using SSR and SNP markers that corresponded to the Chr11 and Chr14 QTL. Accessions showed a range of RKN resistance phenotypes as measured by eggs g−1 root, gall score, and reproductive factor; however, genotypic analyses revealed that all resistant accessions carried either the Chr11 or Chr14 resistance QTL. For RN resistance, G. hirsutum and G. barbadense accessions were investigated. Genotyping of sixteen (16) G. barbadense accessions with the SSR marker BNL3279 that is linked to the Renbarb2 QTL revealed that resistance in these accessions was due to an allele of Renbarb2. Twenty-one (21) G. hirsutum accessions were evaluated for RN resistance as measured by eggs g−1 root, vermiform nematodes g−1 soil, and reproductive factor. None of the G. hirsutum accessions showed a consistent resistant phenotype across multiple experiments. Our findings emphasize the importance of screening new genetically diverse cotton populations in order to find novel sources of RKN and RN resistance.

Kissing Kucek, L.; Mallory, E. B.; Darby, H. M.; Dawson, J. C.; Sorrells, M. E.

doi: 10.1007/s10681-021-02930-9pmid: N/A

Competition from weeds often reduces wheat yields, especially in organic management systems or when herbicide-resistant weeds are present. Breeding wheat for increased competitive ability is an important aspect of integrated weed control. Selecting directly for weed-competitive ability (WCA), however, is challenged by difficult field measurements, genotype by environment interactions, and low heritability. To improve selection efficiency, breeding programs can utilize secondary selection traits that are easier to measure, have higher heritability and are highly correlated with WCA. To identify potential secondary selection traits for WCA, we conducted a meta-analysis of the published literature, and contributed new data from the northeastern United States. Among studies worldwide, early vigor was easy to measure and consistently correlated with WCA. Early plant height also showed promise as a correlated secondary selection trait for WCA, and had high heritability. Tillering, maturity timing, and growth habit were inconsistently correlated with WCA among environments and weed species studied. WCA and the correlated trait of early vigor were influenced by genotype by environment interactions. As a result, decentralized breeding would maximize gain from selection for WCA.

Kissing Kucek, L.; Dawson, J. C.; Darby, H.; Mallory, E.; Davis, M.; Sorrells, M. E.

doi: 10.1007/s10681-021-02905-wpmid: N/A

Although the effect of local adaptation is well documented in evolutionary biology, few studies have quantified the impact of local adaptation in plant breeding. Decentralized plant breeding programs have the potential to harness local adaptation for crop improvement, but the effectiveness of such models is understudied. We quantified the ability of a decentralized participatory plant breeding program to improve Weed-competitive ability (WCA) in organic spring wheat. After four farmers in the northeast United States selected wheat populations for WCA and its correlated trait of early vigor, we tracked gains in selection and local adaptation. On average, farmers enhanced competitive ability of selected genotypes by 11.46%. Measured gains from selection for early vigor and early canopy cover, however, varied among testing environments. Gains in selection were highly related to the genetic correlation coefficient between selection and testing environment (r = 0.77 and r = 0.80 for early vigor and canopy cover, respectively). To accurately measure gains from selection for decentralized breeding programs, testing environments should be chosen that are similar to where selection took place. Inconsistent weed competition among site-years limited conclusions from the analysis of local adaptation for weed competitive ability. Detecting local adaptation in plant breeding, which typically uses a small number of selection cycles compared to evolutionary biology, likely requires many genotypes, environments, and years for adequate statistical power. The ecological complexity of weed competitive ability further complicates experimental design and challenges the ability to measure local adaption.