Genetic variability in 12 butterfly pea (Clitoria ternatea L.) accessions: a dual approach with cluster and principal component analysis

Understanding genetic variability is crucial for enhancing the breeding programs of butterfly pea (Clitoria ternatea L.), particularly in the face of the demand for improved crop varieties. This study aims to (i) evaluate the genetic variability of 12 butterfly pea accessions based on 28 agro-morphological traits and (ii) analyze the genetic relationships among these accessions. The research was conducted from December 2022 to October 2023 at the Ciparanje Experimental Field, Faculty of Agriculture, Universitas Padjadjaran. The experimental design employed a Randomized Complete Block Design (RCBD) with 12 accessions and three replications. Observations were made on 28 agro-morphological traits. Data analysis was performed using analysis of variance (ANOVA), principal component analysis (PCA), and agglomerative hierarchical clustering (AHC). ANOVA results indicated significant diversity among the 12 accessions based on 17 agro-morphological traits. PCA results showed that the first six principal components accounted for 89.1% of the total genetic variability and identified all traits as contributing factors to the genetic variability among the accessions. AHC analysis grouped the accessions into two main clusters, with Euclidean distances ranging from 1.00 to 4.00, indicating varying levels of genetic relatedness. These findings underscore the importance of genetic variability in formulating breeding strategies, particularly in the selection of parents based on targeted agro-morphological traits. ABSTRAK Informasi keragaman genetik sangat penting untuk mendukung program pemuliaan tanaman telang (Clitoria ternatea L.), khususnya dalam menghadapi permintaan varietas unggul. Penelitian ini bertujuan untuk (i) mengevaluasi keragaman genetik dari 12 aksesi kembang telang berdasarkan 28 karakter agro-morfologi dan (ii) menganalisis hubungan genetik di antara aksesi-aksesi tersebut berdasarkan 28 karakter agro-morfologi. Penelitian dilaksanakan pada Desember 2022 hingga Oktober 2023 di Kebun Percobaan Ciparanje, Fakultas Pertanian, Universitas Padjadjaran. Desain eksperimen menggunakan Rancangan Acak Kelompok Lengkap (RAKL) dengan 12 aksesi dan tiga ulangan. Pengamatan dilakukan pada 28 karakter agro-morfologi. Analisis data dilakukan dengan analisis varians (ANOVA), analisis komponen utama (PCA), dan pengelompokan hierarki aglomeratif (AHC). Hasil analisis ANOVA menunjukkan bahwa 12 aksesi telang beragam secara signifikan berdasarkan 17 karakter agro-morfologi. Hasil PCA menunjukkan bahwa enam komponen utama pertama menjelaskan 89,1% dari total keragaman genetik dan mengidentifikasi 28 karakter agro-morfologi sebagai karakter yang berkontribusi terhadap keragaman genetik 12 aksesi telang. Analisis AHC mengelompokkan 12 aksesi menjadi dua kelompok utama dengan jarak Euclidean berkisar antara 1,00 hingga 4,00, mengindikasikan tingkat kekerabatan genetik yang jauh. Temuan ini menegaskan pentingnya keragaman genetik dalam merumuskan strategi pemuliaan yang efektif, terutama dalam pemilihan tetua berdasarkan karakter agro-morfologi yang ditargetkan

Genetic variability in 12 butterfly pea (Clitoria ternatea L.) accessions: a dual approach with cluster and principal component analysis

Understanding genetic variability is crucial for enhancing the breeding programs of butterfly pea (Clitoria ternatea L.), particularly in the face of the demand for improved crop varieties. This study aims to (i) evaluate the genetic variability of 12 butterfly pea accessions based on 28 agro-morphological traits and (ii) analyze the genetic relationships among these accessions. The research was conducted from December 2022 to October 2023 at the Ciparanje Experimental Field, Faculty of Agriculture, Universitas Padjadjaran. The experimental design employed a Randomized Complete Block Design (RCBD) with 12 accessions and three replications. Observations were made on 28 agro-morphological traits. Data analysis was performed using analysis of variance (ANOVA), principal component analysis (PCA), and agglomerative hierarchical clustering (AHC). ANOVA results indicated significant diversity among the 12 accessions based on 17 agro-morphological traits. PCA results showed that the first six principal components accounted for 89.1% of the total genetic variability and identified all traits as contributing factors to the genetic variability among the accessions. AHC analysis grouped the accessions into two main clusters, with Euclidean distances ranging from 1.00 to 4.00, indicating varying levels of genetic relatedness. These findings underscore the importance of genetic variability in formulating breeding strategies, particularly in the selection of parents based on targeted agro-morphological traits. ABSTRAK Informasi keragaman genetik sangat penting untuk mendukung program pemuliaan tanaman telang (Clitoria ternatea L.), khususnya dalam menghadapi permintaan varietas unggul. Penelitian ini bertujuan untuk (i) mengevaluasi keragaman genetik dari 12 aksesi kembang telang berdasarkan 28 karakter agro-morfologi dan (ii) menganalisis hubungan genetik di antara aksesi-aksesi tersebut berdasarkan 28 karakter agro-morfologi. Penelitian dilaksanakan pada Desember 2022 hingga Oktober 2023 di Kebun Percobaan Ciparanje, Fakultas Pertanian, Universitas Padjadjaran. Desain eksperimen menggunakan Rancangan Acak Kelompok Lengkap (RAKL) dengan 12 aksesi dan tiga ulangan. Pengamatan dilakukan pada 28 karakter agro-morfologi. Analisis data dilakukan dengan analisis varians (ANOVA), analisis komponen utama (PCA), dan pengelompokan hierarki aglomeratif (AHC). Hasil analisis ANOVA menunjukkan bahwa 12 aksesi telang beragam secara signifikan berdasarkan 17 karakter agro-morfologi. Hasil PCA menunjukkan bahwa enam komponen utama pertama menjelaskan 89,1% dari total keragaman genetik dan mengidentifikasi 28 karakter agro-morfologi sebagai karakter yang berkontribusi terhadap keragaman genetik 12 aksesi telang. Analisis AHC mengelompokkan 12 aksesi menjadi dua kelompok utama dengan jarak Euclidean berkisar antara 1,00 hingga 4,00, mengindikasikan tingkat kekerabatan genetik yang jauh. Temuan ini menegaskan pentingnya keragaman genetik dalam merumuskan strategi pemuliaan yang efektif, terutama dalam pemilihan tetua berdasarkan karakter agro-morfologi yang ditargetkan

Genetic Diversity of 64 Turmeric Accessions from Indonesia Based on P450-Based Analogue (PBA) Marker

Kunyit merupakan tanaman penghasil rimpang yang memiliki banyak kegunaan, baik untuk konsumsi, industri obat, maupun pewarna. Pengembangan varietas unggul kunyit di Indonesia saat ini perlu didukung oleh adanya informasi keragaman genetik. Saat ini informasi mengenai keragaman genetik tanaman kunyit di Indonesia masih belum tersedia. Salah satu cara untuk memperoleh informasi keragaman genetik adalah dengan menggunakan marka molekuler yang mampu memberikan hasil yang akurat dan tidak dipengaruhi oleh lingkungan. Marka PBA sebagai marka fungsional mampu mendeteksi gen P450 yang berkaitan dengan pembentukan metabolit sekunder pada area genom yang luas sehingga dapat dijadikan alternatif marka untuk mengidentifikasi keragaman genetik. Tujuan dari penelitian ini adalah untuk memperoleh informasi keragaman genetik 64 aksesi tanaman kunyit menggunakan delapan pasang primer P450-Based Analogue (PBA). Penelitian dilakukan di Laboratorium Sentral Universitas Padjadjaran dari Juni 2019 hingga Januari 2020. Sebanyak 133 pita terdeteksi dengan rentang jumlah masing-masing alel 8 – 45 pita, dan rata-rata per alel 22,3 pita. Hasil analisis PIC menunjukkan adanya enam pasang primer PBA yang menunjukkan polimorfisme tinggi pada rentang 0,90 – 0,98 sehingga marka PBA dikategorikan sangat informatif. Analisis klaster membagi 64 aksesi kunyit ke dalam dua klaster utama berdasarkan tingkat kemiripan pada rentang 0,01 hingga 0,83. Aksesi CL-GTL01 yang berasal dari Gorontalo memiliki kemiripan yang rendah yaitu 0,01 terhadap 64 aksesi lainnya, sedangkan aksesi CL-NTB01 dan CL-PPB04 memiliki tingkat kemiripan yang tinggi pada jarak 0,83. Berdasarkan nilai PIC, jumlah pita polimorfik, dan jarak genetik, kunyit asal Indonesia memiliki keragaman yang luas berdasarkan marka PBA. Turmeric is a rhizome producing plant with many utilization such as for consumption, medicine, and colorant industries. The development of superior turmeric varieties in Indonesia needs to be supported by genetic diversity information availability. Despite its potential, genetic diversity information of Indonesian turmeric has not been widely observed. A molecular marker is used to address genetic diversity information with the accurate result due to minimum environmental influences. PBA can detect the P450 gene as a functional marker, which is related to the synthesis of secondary metabolites in a wide genome area.  Thus, it can be used as an alternative marker to identify genetic diversity. This research aimed to obtain genetic diversity information of 64 turmeric accessions using eight primer sets of P450-Based Analogue (PBA). The study was conducted in the Central Laboratory of Padjadjaran University from June 2019 to January 2020. Results showed that the full 133 bands were detected with a range of allele number 8 - 45 bands and an average of 22.3 bands per allele. PIC analysis showed six primer sets of PBA had high polymorphisms ranged from 0.90 to 0.98, hence categorized PBA as a highly informative marker. Cluster analysis divided 64 turmeric accessions into two main clusters based on a similarity index ranged from 0.01 to 0.83. The accession of CL-GTL01 origins from Gorontalo had a low similarity coefficient of 0.01 to the other 64 accessions cluster. On the other hand, CL-NTB01 dan CL-PPB01 had the highest similarity index of 0.83. Based on the PIC value, the total number of polymorphic bands, and genetic distance, it can be concluded that local Indonesian turmeric had wide diversity based on PBA marker

Separate loci underlie resistance to root infection and leaf scorch during soybean sudden death syndrome

Soybean [Glycine max (L.) Merr.] cultivars show differences in their resistance to both the leaf scorch and root rot of sudden death syndrome (SDS). The syndrome is caused by root colonization by Fusarium virguliforme (ex. F. solani f. sp. glycines). Root susceptibility combined with reduced leaf scorch resistance has been associated with resistance to Heterodera glycines HG Type 1.3.6.7 (race 14) of the soybean cyst nematode (SCN). In contrast, the rhg1 locus underlying resistance to Hg Type 0 was found clustered with three loci for resistance to SDS leaf scorch and one for root infection. The aims of this study were to compare the inheritance of resistance to leaf scorch and root infection in a population that segregated for resistance to SCN and to identify the underlying quantitative trait loci (QTL). “Hartwig”, a cultivar partially resistant to SDS leaf scorch, F. virguliforme root infection and SCN HG Type 1.3.6.7 was crossed with the partially susceptible cultivar “Flyer”. Ninety-two F5-derived recombinant inbred lines and 144 markers were used for map development. Four QTL found in earlier studies were confirmed. One contributed resistance to leaf scorch on linkage group (LG) C2 (Satt277; P = 0.004, R 2 = 15%). Two on LG G underlay root infection at R8 (Satt038; P = 0.0001 R 2 = 28.1%; Satt115; P = 0.003, R 2 = 12.9%). The marker Satt038 was linked to rhg1 underlying resistance to SCN Hg Type 0. The fourth QTL was on LG D2 underlying resistance to root infection at R6 (Satt574; P = 0.001, R 2 = 10%). That QTL was in an interval previously associated with resistance to both SDS leaf scorch and SCN Hg Type 1.3.6.7. The QTL showed repulsion linkage with resistance to SCN that may explain the relative susceptibility to SDS of some SCN resistant cultivars. One additional QTL was discovered on LG G underlying resistance to SDS leaf scorch measured by disease index (Satt130; P = 0.003, R 2 = 13%). The loci and markers will provide tagged alleles with which to improve the breeding of cultivars combining resistances to SDS leaf scorch, root infection and SCN HG Type 1.3.6.7

Pathotype Diversity of Phytophthora sojae in Eleven States in the United States

Pathotype diversity of Phytophthora sojae was assessed in 11 states in the United States during 2012 and 2013. Isolates of P. sojae were recovered from 202 fields, either from soil samples using a soybean seedling bioassay or by isolation from symptomatic plants. Each isolate was inoculated directly onto 12 soybean differentials; no Rps gene or Rps 1a, 1b, 1c, 1k, 3a, 3b, 3c, 4, 6, 7, or 8. There were 213 unique virulence pathotypes identified among the 873 isolates collected. None of the Rps genes were effective against all the isolates collected but Rps6 and Rps8 were effective against the majority of isolates collected in the northern regions of the sampled area. Virulence toward Rps1a, 1b, 1c, and 1k ranged from 36 to 100% of isolates collected in each state, while virulence to Rps6 and Rps8 was less than 36 and 10%, respectively. Depending on the state, the effectiveness of Rps3a ranged from totally effective to susceptible to more than 40% of the isolates. Pathotype complexity has increased in populations of P. sojae in the United States, emphasizing the increasing importance of stacked Rps genes in combination with high partial resistance as a means of limiting losses to P. sojae

Unused Natural Variation Can Lift Yield Barriers in Plant Breeding

Natural biodiversity is an underexploited sustainable resource that can enrich the genetic basis of cultivated plants with novel alleles that improve productivity and adaptation. We evaluated the progress in breeding for increased tomato (Solanum lycopersicum) yield using genotypes carrying a pyramid of three independent yield-promoting genomic regions introduced from the drought-tolerant green-fruited wild species Solanum pennellii. Yield of hybrids parented by the pyramided genotypes was more than 50% higher than that of a control market leader variety under both wet and dry field conditions that received 10% of the irrigation water. This demonstration of the breaking of agricultural yield barriers provides the rationale for implementing similar strategies for other agricultural organisms that are important for global food security

Geographic Distribution of Soybean Aphid Biotypes in the United States and Canada during 2008–2010

Soybean aphid (Aphis glycines Matsumura) is a native pest of soybean [Glycine max (L.) Merr.] in eastern Asia and was detected on soybeans in North America in 2000. In 2004, the soybean cultivar Dowling was described to be resistant to soybean aphids with the Rag1 gene for resistance. In 2006, a virulent biotype of soybean aphid in Ohio was reported to proliferate on soybeans with the Rag1 gene. The objective was to survey the occurrence of virulent aphid populations on soybean indicator lines across geographies and years. Nine soybean lines were identified on the basis of their degree of aphid resistance and their importance in breeding programs. Naturally occurring soybean aphid populations were collected in 10 states (Kansas, Illinois, Indiana, Iowa, Michigan, Minnesota, North Dakota, Ohio, South Dakota, and Wisconsin) and the Canadian province of Ontario. The reproductive capacity of field-collected soybean aphid populations was tested on soybean lines; growth rates were compared in no-choice field cages at each geographic region across 3 yr. The occurrence of soybean aphid biotypes was highly variable from year to year and across environments. The frequency of Biotypes 2, 3, and 4 was 54, 18, and 7%, respectively, from the 28 soybean aphid populations collected across 3 yr and 11 environments. Plant introduction (PI) 567598B, a natural gene pyramid of rag1c and rag4, had lowest frequency of soybean aphid colonization (18%). Several factors may have contributed to the variability, including genetic diversity of soybean aphids, parthenogenicity, abundance of the overwintering host buckthorn (Rhamnus spp.), and migratory patterns of soybean aphids across the landscape